I had the same issue except it was my amp. I replaced the amp and now my system works great. See if your amp is in protection mode next time that happens if u can't find a wiring issue.
I had the same issue a few years ago...took the amp to Rockford and they looked it over, decided that there was an internal problem and gave me an updated BD1000.1(the current amp I have). Havent had a problem since then.