OP, give us your full Equipment List.
Head Unit:
Front Speakers:
Rear Speakers:
Sub(s):
Amplifier:
Processors if any:
Also, do you know what size wire guage is run to each speaker (assuming/hoping the Sub is larger than the rest). Are you using Factory speaker wire or all new runs? If Factory how and where are you tying into them?
Be Specific with the model numbers. Everyone is making guesses at what might be happening because we don't have enough information to go by. Can't troubleshoot correctly if we don't know Exactly what it is we're troubleshooting.