I have the same amp, how do you have the subs wired and are they dual or single voice coil?
I had my 2 dual voice coil subs wired up at 1 ohm for a short while, I had the same problem. Wired them up at 2 ohm and it fixed the whole problem. It's a good strong amp, haven't had a problem out of mine for 3 years now, and that's saying something for me.