Having issues with my keyboard on my Macbook Pro. The option key and command key have swapped functions and I can't switch it back. Tried keyboard settings (modifier keys and keyboard shortcuts) in system preferences and everything appears to be set properly. Tried doing a safe boot to clear out cache (?), deleting com.apple.systempreferences.plist and com.apple.keyboard.plist but no effect.
Sounds to me like you perhaps downloaded a application that swaps these keys, it's the only thing I can think of. But then again, if you do a safe boot and this problem still exists this shouldn't happen.
If you boot from the install disk that came with your computer and start one of the utilities from the menu, are the keys still switched? Just trying to figure out if anything has changed on your system drive or if it's some other problem.
Mac Pro, 4x3 Ghz, 8 Gb ram, ATI 1900XT, KONA 3, Sony PVM20L4, Tangent Devices Wave.