Originally Posted by cheshirecat

You could also check the individual rca jacks to see if they're a bit loose. If an installer puts too much pressure on an individual jack and breaks the ground, you can get signal loss until the unit heats up and the metal expands, creating the connection. The car bouncing around may cause intermittent loss here also.

But again, as far as the key fob goes, that's really weird. I still think there's some kind of electrical issue going on there. I haven't heard anything at all about aftermarket systems putting out any kind of signal strong enough to keep the fob from working, but there's always a first time for everything.