Leave it to Microsoft...
The command keys in Word 2004 for Mac seem to read as qwerty. Command-F, for example, gets read as Command-E. This only happens with Word + Colemak; all other programs read Colemak command keys just fine, and Word reads Dvorak keys just fine.
I'm picturing the whole set of preinstalled Mac layouts coded somewhere in Word, and handled through its own input system completely bypassing the Mac OS. That strikes me as about par for the course for Microsoft. Still, if anyone knows a way around this, I'd love to hear it.