One other thing to try and meant to mention in earlier response is to go to the ..\MAME\CFG\ directory and rename/delete the "default.cfg" and try again. In theory it regens the default file automatically but something to verify. Also check in same directory that the game you are testing doesn't have any unwanted controller mappings in it. Beyond that not sure why wouldn't be taking the CTRLR file (whatever you decide on using) as primary other than trying a vanilla install of MAME in test directory somewhere and working backwards.