Unfortunately this sounds like a Q.921 problem, and there aren't an abundant amount of ways to troubleshoot it.
The first thing you can try doing is removing MGCP configuration because Q.921 becomes tied into CUCM registration, and makes the entire thing very complex.
If you're having the issue with H323/SIP, it means there is a bonafide circuit problem. If it doesn't happen with H323, you will want to try restarting the CCM service, resetting the gateway in CUCM, removing the 'isdn bind-l3 ccm' command, or doing a 'no mgcp' 'mgcp' on the gateway. You're seeing erratic behavior most likely associated with a bug or flaky CUCM registration.
hth,
nick