After removing the programming for the lights the system ran relatively smoothly all night last night, so it seems we may have identified the issue. I don't really understand why this would trigger the behavior we were seeing as basically the amounted to one of three LED lights being on all the time.
I've started a few new threads to discuss the hook ups on our interface kit to ensure that nothing was done incorrectly:
viewtopic.php?f=5&t=9921&p=31512#p31512
viewtopic.php?f=5&t=9918&p=31498#p31498
viewtopic.php?f=5&t=9922