I don't see how you can have two files named BGMAIN.EXE in the same folder. Are you sure that one of them isn't called BGMAIN2.EXE or something like that?
I use an experience cap remover that goes into the /OVERRIDE directory. You can download it
here. It's the one called "Baldur's Gate XP Cap Disabler". Instead of removing the experience cap, it sets the experience cap for all of the classes to -1, which effectively disables it. No fuss, no mess.
There's also one called "Godlike", but I wouldn't use any type of crack that overwrites or modifies my BGMAIN.EXE file.