Sometimes clamps will pull cylinders out of alignment when tightened. It just depends, I think a new C-clip thing can help in that situation.
Try checking these things -
Can you get a full range of adjustment with the clamps loose? If not, you may need to file the slots in your mounts.
Do the pistons move when you've tighened the mounts? If so, your bolts may be bottoming out, try putting washers on top of the mounts, or (be careful!) cutting your bolts down a bit.
And finally the original point, do the pads stop being square to the rim when you fully tighten the clamps? Replacing the plastic C-clip thing can help, You might also want to try filing the mounts so they are all level with each other - http://www.youtube.com/watch?v=NEezZeqmVO8.
Post back with results!