Acid Pro etc Processing

[Ally]

I've got a certain audio file that's been processed (rendered to mp3 or WAV) several times through each iteration of working on it. When playing on CD Audio through a very good stereo system I've noticed that aside from an obvious reduction in quality the sound seems to be leaning a lot further to the bass end of the scale, such that say a section of rock music sound now has that house 'hoover' sound accompanying it - is this an effect phenomenom anyone else notices and can anyone recommend a method of cleaning up this audio beyond skewing the EQ to compensate?

Thanks,
-Ally