External keyboard and modifier keys

I like to swap my "Ctrl" and "Command" modifiers keys and I've never had a problem doing this until upgrading to Lion.  If I disconnect and reconnect my external keyboard sometimes my modifier keys are reset.
Lion lets you change modifier keys per keyboard which is where I think the problem lies.  I also have duplicate listings for my external keyboard and I'm not sure how to delete the duplicates.
Does anyone know how to fix these issues?

Also, I'm not sure if it matters but my mouse and keyboard are connected through a USB hub which then connects to the Macbook Air.

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