sub is cutting off at high volume, help

OK, got my system installed last Friday and it's HUGE! I have four speakers in the boat running on a JL 4350, six tower speakers running on JL 6450, one JL 13W6V2 sub in a downfire box running on a JL 1000/1 amp. I have a two battery setup, they are interstate marine cranking batteries. Stinger SR200 isolator. The deck is still powered off the main battery but everything else runs off the second, radio battery. It is carrying a constent 13V so no battery issues. But at high volumes the Sub quits playing when you turn the volume back down it starts back up. Anyone had this issue and how did you overcome it?

Thanks for your responses,
Ken