Sounds to me like the new placement of the speakers is affecting the sound quality. Don't forget that your M60s are ported front and rear so placement can make a big difference. How far away from walls and other furniture are they? Even giving the rear ports an extra 4 or 6 inches to breath may affect the quality of sound. Are they close to side walls or in a corner? Try moving them around a bit. I'm guessing your Paradigm bookshelves are not ported.

-Dave