Hi Merrick,
I don't have the 33120A to test your problem with, but I do have a couple of suggestions:
1) Is it possible that one of the configuration vi's is being called in a loop? If the pulse train is the same length as expected for the pulse length, then it sounds like the SYNC TTL output is being set and reset, possibly from calling it in a loop.
2) Make sure that a clock is not selected as a source for the TTL pulse.
If you are still having issues, please post a screenshot of your vi and maybe we can find the source of the error.