[MayaInstallPath]\scripts\startup\hotkeySetup.mel I've had this issue with certain keys, I've been able to comment out most of the offenders in this file, but could not override ctrl-w for the life of me. I've some viewport shading scripts that stop functioning if I even click on the 'shading' panel menu. It could be…
I've looked into editing a few script files, but maybe I need to dig deeper. And yea, like you with ctrl+w, it seems certain specific hotkeys seem to be more troublesome than others. (Read : Anything with Z) When I first started to learn Maya, a friend gave me his setup and I grew to really like it. But your right, maybe…