I have two 10"inch subs and the amp is 1000watts, when the volume is up the subs turn off and on. The amp is turned all the way down just because I am trying to break in the subs.
it sounds like the amp is overheating. either that or it's a bad ground. I'd check your grounds first, however. remove them, scrape the paint or metal with a screwdriver to be sure your contacting metal, re-attach. try it then, and make sure your grounds to everything else are real tight.
Before anything I'd check to make sure your running the subs at a stable amount of ohms. I had this problem before when i was running my setup at 2 ohms stupidly. After i wired them down to 4 ohms the problem stopped.