I didn't have to install any new files with my MPD32. I just plugged it in, setup Reason to recognize it, and it worked. I didn't have to change any of the Remote files. (I'm on a PC, so if you're on a Mac, this might not apply to you. I don't know.)
Make sure preset 2 (I think) is loaded in the MPD32 and give it another shot. If that's not the problem, I would delete the files you installed and re-launch Reason. It should replace the missing files with the default files.
If that STILL doesn't work, first check to see that the files were replaced. If they were, the MPD32 might be sending the wrong MIDI messages. You should be able to reset the controller to factory default. Just do a sysex dump first if you made any changes to it you want to keep.
"Bleach is mostly water, we are mostly water, therefore, we are bleach." - Nathan Explosion