I set the SPA303 config setting "RFC2543 Call Hold" from yes to no, and also added <param name="rtp-autofix-timing" value="false"/> to my internal.xml sip profile. The errors went away but the issue persists.
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:40.908307 [DEBUG] switch_channel.c:1831 (sofia/internal/1001@192.168.0.114:5060) Callstate Change ACTIVE -> HELD
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.158321 [DEBUG] switch_core_media.c:4153 Audio Codec Compare [PCMU:0:8000:30:64000:1]/[PCMU:0:8000:30:64000:1]
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.158321 [DEBUG] switch_core_media.c:4208 Audio Codec Compare [PCMU:0:8000:30:64000:1] ++++ is saved as a match
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.158321 [DEBUG] switch_core_media.c:4153 Audio Codec Compare [PCMA:8:8000:30:64000:1]/[PCMU:0:8000:30:64000:1]
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.158321 [DEBUG] switch_core_media.c:4069 Set telephone-event payload to 101@8000
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.158321 [DEBUG] switch_core_media.c:4417 Set telephone-event payload to 101@8000
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.158321 [DEBUG] switch_core_media.c:4473 sofia/internal/1001@192.168.0.114:5060 Set 2833 dtmf send payload to 101 recv payload to 101
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.158321 [DEBUG] switch_core_media.c:6010 Audio params are unchanged for sofia/internal/1001@192.168.0.114:5060.
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.158321 [DEBUG] sofia.c:7503 Processing updated SDP
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.168322 [DEBUG] sofia.c:6756 Channel sofia/internal/1001@192.168.0.114:5060 entering state [completed][200]
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:06:41.178318 [DEBUG] sofia.c:6756 Channel sofia/internal/1001@192.168.0.114:5060 entering state [ready][200]
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.288104 [DEBUG] sofia.c:6756 Channel sofia/internal/+14196680795@184.106.123.160 entering state [terminating][0]
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.288104 [NOTICE] sofia.c:7775 Hangup sofia/internal/+14196680795@184.106.123.160 [CS_EXECUTE] [NORMAL_UNSPECIFIED]
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.288104 [DEBUG] switch_ivr_bridge.c:705 sofia/internal/+14196680795@184.106.123.160 ending bridge by request from read function
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.288104 [DEBUG] switch_ivr_bridge.c:778 BRIDGE THREAD DONE [sofia/internal/+14196680795@184.106.123.160]
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [DEBUG] switch_ivr_bridge.c:778 BRIDGE THREAD DONE [sofia/internal/1001@192.168.0.114:5060]
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [DEBUG] switch_channel.c:2019 (sofia/internal/1001@192.168.0.114:5060) Callstate Change HELD -> UNHELD
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [NOTICE] switch_ivr_bridge.c:881 Hangup sofia/internal/1001@192.168.0.114:5060 [CS_EXCHANGE_MEDIA] [NORMAL_CLEARING]
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [DEBUG] switch_core_state_machine.c:542 (sofia/internal/1001@192.168.0.114:5060) State EXCHANGE_MEDIA going to sleep
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [DEBUG] switch_core_state_machine.c:473 (sofia/internal/1001@192.168.0.114:5060) Running State Change CS_HANGUP
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [DEBUG] switch_core_state_machine.c:739 (sofia/internal/1001@192.168.0.114:5060) Callstate Change UNHELD -> HANGUP
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [DEBUG] switch_core_state_machine.c:741 (sofia/internal/1001@192.168.0.114:5060) State HANGUP
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [DEBUG] mod_sofia.c:431 Channel sofia/internal/1001@192.168.0.114:5060 hanging up, cause: NORMAL_CLEARING
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.318106 [DEBUG] switch_ivr_bridge.c:1689 sofia/internal/1001@192.168.0.114:5060 skip receive message [UNBRIDGE] (channel is hungup already)
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.318106 [DEBUG] switch_ivr_bridge.c:1692 sofia/internal/+14196680795@184.106.123.160 skip receive message [UNBRIDGE] (channel is hungup already)
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.318106 [DEBUG] switch_core_session.c:2796 sofia/internal/+14196680795@184.106.123.160 skip receive message [APPLICATION_EXEC_COMPLETE] (channel is hungup already)
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.318106 [DEBUG] switch_core_state_machine.c:539 (sofia/internal/+14196680795@184.106.123.160) State EXECUTE going to sleep
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.318106 [DEBUG] switch_core_state_machine.c:473 (sofia/internal/+14196680795@184.106.123.160) Running State Change CS_HANGUP
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.318106 [DEBUG] switch_core_state_machine.c:739 (sofia/internal/+14196680795@184.106.123.160) Callstate Change ACTIVE -> HANGUP
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.318106 [DEBUG] switch_core_state_machine.c:741 (sofia/internal/+14196680795@184.106.123.160) State HANGUP
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.318106 [DEBUG] mod_sofia.c:431 Channel sofia/internal/+14196680795@184.106.123.160 hanging up, cause: NORMAL_UNSPECIFIED
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.328100 [DEBUG] mod_sofia.c:484 Sending BYE to sofia/internal/1001@192.168.0.114:5060
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:60 sofia/internal/1001@192.168.0.114:5060 Standard HANGUP, cause: NORMAL_CLEARING
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:741 (sofia/internal/1001@192.168.0.114:5060) State HANGUP going to sleep
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:508 (sofia/internal/1001@192.168.0.114:5060) State Change CS_HANGUP -> CS_REPORTING
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:473 (sofia/internal/1001@192.168.0.114:5060) Running State Change CS_REPORTING
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:827 (sofia/internal/1001@192.168.0.114:5060) State REPORTING
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:104 sofia/internal/1001@192.168.0.114:5060 Standard REPORTING, cause: NORMAL_CLEARING
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:827 (sofia/internal/1001@192.168.0.114:5060) State REPORTING going to sleep
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:499 (sofia/internal/1001@192.168.0.114:5060) State Change CS_REPORTING -> CS_DESTROY
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_session.c:1646 Session 3 (sofia/internal/1001@192.168.0.114:5060) Locked, Waiting on external entities
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [NOTICE] switch_core_session.c:1664 Session 3 (sofia/internal/1001@192.168.0.114:5060) Ended
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [NOTICE] switch_core_session.c:1668 Close Channel sofia/internal/1001@192.168.0.114:5060 [CS_DESTROY]
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:630 (sofia/internal/1001@192.168.0.114:5060) Running State Change CS_DESTROY
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:640 (sofia/internal/1001@192.168.0.114:5060) State DESTROY
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] mod_sofia.c:341 sofia/internal/1001@192.168.0.114:5060 SOFIA DESTROY
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:111 sofia/internal/1001@192.168.0.114:5060 Standard DESTROY
f9765406-acd9-480c-a200-43bdc2ad2f36 2016-01-14 12:07:12.338101 [DEBUG] switch_core_state_machine.c:640 (sofia/internal/1001@192.168.0.114:5060) State DESTROY going to sleep
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_state_machine.c:60 sofia/internal/+14196680795@184.106.123.160 Standard HANGUP, cause: NORMAL_UNSPECIFIED
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_state_machine.c:741 (sofia/internal/+14196680795@184.106.123.160) State HANGUP going to sleep
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_state_machine.c:508 (sofia/internal/+14196680795@184.106.123.160) State Change CS_HANGUP -> CS_REPORTING
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_state_machine.c:473 (sofia/internal/+14196680795@184.106.123.160) Running State Change CS_REPORTING
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_state_machine.c:827 (sofia/internal/+14196680795@184.106.123.160) State REPORTING
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_state_machine.c:104 sofia/internal/+14196680795@184.106.123.160 Standard REPORTING, cause: NORMAL_UNSPECIFIED
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_state_machine.c:827 (sofia/internal/+14196680795@184.106.123.160) State REPORTING going to sleep
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_state_machine.c:499 (sofia/internal/+14196680795@184.106.123.160) State Change CS_REPORTING -> CS_DESTROY
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [DEBUG] switch_core_session.c:1646 Session 1 (sofia/internal/+14196680795@184.106.123.160) Locked, Waiting on external entities
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [NOTICE] switch_core_session.c:1664 Session 1 (sofia/internal/+14196680795@184.106.123.160) Ended
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.348102 [NOTICE] switch_core_session.c:1668 Close Channel sofia/internal/+14196680795@184.106.123.160 [CS_DESTROY]
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.358102 [DEBUG] switch_core_state_machine.c:630 (sofia/internal/+14196680795@184.106.123.160) Running State Change CS_DESTROY
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.358102 [DEBUG] switch_core_state_machine.c:640 (sofia/internal/+14196680795@184.106.123.160) State DESTROY
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.358102 [DEBUG] mod_sofia.c:341 sofia/internal/+14196680795@184.106.123.160 SOFIA DESTROY
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.358102 [DEBUG] switch_core_state_machine.c:111 sofia/internal/+14196680795@184.106.123.160 Standard DESTROY
9cbfdabc-8f1f-4fb3-89f2-c1b0c8522c5c 2016-01-14 12:07:12.358102 [DEBUG] switch_core_state_machine.c:640 (sofia/internal/+14196680795@184.106.123.160) State DESTROY going to sleep