Sounds like you need more juice for your subs. Question though does the music totally turn off or just the sub stop working? Check the amp and see if its really hot, just becareful. If it is hot, you might have found the answer to your problem, more power is needed.
HU: Kenwood CD w/ Kenwood Chg
FRONTS: Kenwood DB+ Excelon 2-way 6.5"
REAR: Kenwood 3-way
MID/HI AMP: 400x4 Fosgate Punch
SUB: 12' Kicker VR
SUB AMP: 250x2 Fosgate Punch
**Soon to come... anything but those front Kenwoods, possibly Infinity Perfect Seperates