Calvin,
Did you ever get the problem solved? I have a 2003 BMW 330CI and is experiencing similar problems despite all my best efforts for 2 months of tuning.
My system:
JL 450/4
JL 500/1
JL Audio 5.25 coaxial front with image tweeters and CDT audio coaxial rear
JL 10W6V2 in a sealed box...