If it works with the baseline code, then hardware issues are unlikely (the base modules that ship with JeVois exercise it very thoroughly). Maybe your issue is that you are sending some text messages out of the serial-over-USB port, but that port starts blocking after a while if there is nobody on the host computer to listen to the messages.
If you have a script.cfg file in your module's directory, or if you have mofified initscript.cfg in JEVOIS:/config/ on your microSD card, make sure you have
setpar serout Hard
setpar serlog None
and also check for params.cfg in the module's directory. Have a look at this related post:
http://jevois.org/qa/index.php?qa=1712&qa_1=video-output-freezes-on-two-different-camera