Are you using the LFO's on the VCA?
This will overide everything else and when you stop the lfo will continue to open and close the VCA making sounds continue and i guess glitching if its a fast LFO.
It also sounds like you have a USB ground loop, try using some other ports on your PC/MAC, if its a laptop you may need to get little box i think they sell that eridicates the ground loop or you can look online for other tips how to alliviate.
Check if your using the VCA on any LFO's, do this with no USB so any ground loop isnt effecting things, then get back to us and let us know if this is one cause of your problems.
Also make sure you are updated to the latest OS you can find in the sticky threads at the top of the forum.