Well, this isn't entirely accurate. Like Mike J said, if you dialed something like this at the CLI:

pa call sip:user@domain.com

Then you'd need the dialplan entry that handles the SIP URI.

Going back to the original question...
X-Lite dials 1009@4.2.2.2 correct?
But you're saying that the dialplan simply sees "1009" as the destination number? I'm looking at the pastebin (10089) and trying to figure out exactly what is happening. All I can see is that you have a context named "Global" so I'm assuming you've made at least some modifications to the default dialplan. Can you pastebin that whole context?

The other thing that you should probably do is create an extension in this global context that routes a call to the info application. You could do something like this so that "9992" would do an info dump:
<extension name="info">
  <condition field="destination_number" expression="^(9992)$">
    <action application="info"/>
  </condition>
</extension>

Then reloadxml and make a call to 9992 from your X-Lite client. The CLI will have a dump and you'll see all sorts of variables listed. Many of those are available for you to use for condition matches and routing in the dialplan.

Let us know how the info application does in giving you information about the A leg of the call.
-MC