interference

Turn the gains down, this is what it sounds like to me, if you have a bass boost turned up, turn it down as well. Like Dyohn suggested, make sure you have a really good ground for that amp and are using the proper guage wire for both power and ground.

An amp is designed to get hot but not too hot. When the heat cannot be dissipated properly the amp will go into thermal protection. Here is another thing to consider, in the evening and during the day your vehicle is usually much warmer on the inside than first thing in the morning, thus the level of heat to be removed from an already warm amp is even more of a problem in a warm trunk.

Also if it went into protection it could be the impedence load on the amp.  How are the speakers wired and what it the total impedence load?  What are the model numbers of the equipment you're running?

And as we seem to constatly have to preach, set your gains PROPERLY and if you don't understnad what that means, do a search on the forum (since the instructions have been posted here hundreds of times) or ask!

That is a good thing actually, a gain is designed to be turned down. It is not a volume control, it is a a matching device for the different cd players that haev different output voltages. This is more of a bad match of amplifiers and subs, what you are doing is trying to use a Chevy Cavalier engine to power a Western Star. I'm sure you get the drift now. The amp is book rated as 800w x1 @ 4 ohm mono load, this is a little bit of a stretch for power output to say the least. Here is how I would wire your subs to your amp to prevent the amp from going into protection due to low impendence, this will not however stop the amp from going into thermal protection, what you need if you want it loud, is a much larger amp.

Wiring Option #2