Keyboard modifier key remap suddenly not working

I am using a MacBook Pro running OS X 10.6.8 (Snow Leopard). I use a third-party USB keyboard that is laid out (naturally) Windows-style, with the Alt keys inside (closer to the space bar than) the “Windows logo” keys. I use the Modifier Keys button in the Keyboard preference panel to remap these to the standard Mac configuration, with the Command keys on the inside and the Option keys on the outside.
Today those modifier keys are suddenly reversed back to the default Windows layout. The Keyboard panel still shows my preferred (remapped) configuration, but it is not being honored. I have tried reverting to the default layout and then back again, I have rebooted the system, nothing works—the modifier keys are still stuck in the Windows configuration. I rely heavily on keyboard macros in my work, most of which use the modifier keys, and those keystrokes are built into my fingers as second nature. The reversed modifier keys are driving me crazy. Please help: what can I do to make the keyboard honor my settings in the Keyboard preference panel?

Same problem here. Been working fine for a couple years and now suddenly the modifier key mapping is being ignored.

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Keyboard modifier key remap suddenly not working

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