Cmd-W in OSX is default for close window, so that's probably it. You say you've tried to fix it.. Have you tried these? In Terminal.app, find the setting for

Cmd-W in OSX is default for close window, so that's probably it. You say you've tried to fix it.. Have you tried these? In Terminal.app, find the setting for "don't close this window unless no commands are running", and select it. Or, in System Prefs/Keyboard/mappings or somesuch, override Cmd-W in Terminal.app to a noop.