Seems like everyone is pointing you in the right direction. The issue with the pads having a top and bottom is something to check, I know because I have assembled the rear end on my MRX4 many times. I would not sand the pads to much after assembly because if you run the car you want the pads to seat properly. The pads should only slightly touch the disc with some play until engaged. Sounds like you need to check your rear end/brake assembling.
Check the date on this thread... 3 years ago.