is it disconecting, or is it resetting?
most mods have only been completly tested with microsoft controlers. if you have a third party, I am not sure where to start.
disconecting:
did you do the sleeper mod, conected to the sinc button? if so disconect it and see if the problem goes away.
resetting:
is there anychance you bridged the top and center pin?
thoses would be my first two steps. but like I said, with 3rd party controllers, I am not 100% sure, just shooting in the dark. could be a poor wrote code,put open source in it see what happens