Tiger-Heli,
I have run into the same issue. Having Joystick=1 without a joystick plugged in can cause strange keyboard issues. In my case it was like up and left would get stuck on.
Truz,
Like TH said, Try comparing your mame.ini and mame.cfg files to see if there are any settings that are different. If there are, that might be the one that is screwing things up.