Check what you are recieving as dialled string, we had a similar issue and it transpired that the SIP provider was sending the account number rather than the DDI, so call was not following expected route via the DID Table.
If you program a handset to show all lines, then call in on the number in question so that you know which trunk the call is on, then immediately look in system management, trace, co line status for the corresponding line you will be able to see the string that has been presented