You did remember to save after editing the controls?
First things that comes to mind is that your profiles somehow got corrupted.
Try deleting them and start over, take a copy of them first if you want just in case.
In the actionmapper you could try to create a new profile and see how that works out.
I had trouble with mine and found the solution was to simply create a new "default" profile and map everyhting from there, though I use the X52.