Ive had and still do have the same problem when changing to use a pad for the srv, was also useing the pad for the new camera system but not used it since it came out due to the above problem.
I even tried backing up the file and rewritting it after the last time it happend, if I rem right that did the trick, or it did most of it, still think there were a few that needed remapping, thankfully only play on M/KB so wasnt as many as some who might play with JS/Throttle..
+one from me on the need for more than one savable bindings thingie...