Option and Command Key Swapped on Built-in Keyboard

My option and command keys are swapped on the built in keyboard. They work fine with a external USB keyboard. I have checked that the keyboard & mouse > modifier keys preference and they aren't remapped in there. In fact, changing the mapping in there has no affect on the command and option keys.
Any suggestions? Is there a plist file that I can trash?
Thanks

I was finally able to fix this by plugging in my non-Apple external keyboard. Once I did this, a drop down menu appeared in the modifier keys window that let me select the internal MacBook keyboard and fix the mapping issue.

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