I have not experienced any tone problems with mine. The problem I'm having now is with my Byers guitar, because of the slant on the upper bout of the soundboard. The two rearmost (towards the waist) contact surfaces grab the guitar but the upper ones make no contact. I have a few ideas on how to modify it, but then it will not work with my other guitars ( can't win'em all !)
. However, the problem you are having does not ocurr on any of my three guitars. One fix could be to make the contact surfaces shorter so it only makes pressure closer to the glued edge of the soundboard and binding. I also had the same rewarding experience on my lower back and I also prefer the rubber protected clamp to the suction cups.
Hope you find a fix.