best guess is that there is an issue between what you have and what you are trying to play.
there could be a passive filter filtering out bass to four of the six speakers, and you might not have the subwoofer speakers connected.
there could be a factory amp that does tee same thing again.
there could be factory amplifeirs that when you used the amps you have now clip the bejesus out of the amp and reduce audible response in bass frequencies.
maybe your bass speakers are blown.
either way, its probbaly either a filter issue, or a damaged equipment issue.
or a tuning issue. maybe the amp is set to highpass at 250 Hz.