Audio Systems: Problems with stereo output for amp/subwoofer?, sony xplode, bmw z4

Question
I have a Sony Xplode 1200W 12" subwoofer powered by a Rockford Fosgate 900W amp. I just recently had it removed from my Mitusubishi Eclipse Spyder and installed in my BMW Z4. The installers tell me that the subwoofer isn't working in the Z4 because the output from the factory stereo isn't as strong as it was in the Eclipse.  Could this be true?  I thought that's what the amp was for!  Thanks for your help.

Answer
sounds like BS to me!  the amp should have a gain knob on it to compensate even if this was true.  And if the BMW's output was less, the sub would just be quieter, it wouldnt just not work all together.
They either busted something and are trying to cover it up or they simply have no idea what they're doing.