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I use Lion at work with an MS Natural Ergonomic Keyboard 4000. Every single time I log in I have to go into settings and swap the command and control keys. This is really annoying. Is there a way to get these settings to stick?

Beyond that, I'd also like to remap a few other keys and I'm interested in tools for doing that. I think I need to work out the first issue first though.

Thanks for any help.

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I'm having this same problem on Mavericks now too -- every time my MBP goes to sleep or reboots, it "forgets" that I had swapped Modifier Keys! –  ewall Nov 7 '13 at 4:18
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Well i use an apple keyboard, so i have no idea why the switching of cmd & ctrl doesn't stick.

But you might have better luck trying KeyRemap4Macbook, which contrary to it's name works with all keyboards on any mac. Especially PC keyboards. Really designed for these sort of things.

For changing the standard keys i use Ukelele which has a far better GUI and produces a standard keylayout xml OSX understands natively.

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