I've got a Microsoft Natural Ergonomic Keyboard 4000, with the latest IntelliType drivers installed. There is an option to swap a Caps Lock and a Control key in the Microsoft Keyboard preferences pane, but no way to use Caps Lock as a second Control key.
Changing the Modifier Keys in System Preferences > Keyboard helps, but resets after the restart. Reset happens only when Microsoft Keyboard Helper is launched. These settings were always saved after the restart with another third-party keyboard I've been using before.
Using ControllerMate helps, but it's slow, buggy and, obviously, a huge overkill for my needs.
KeyRemap4MacBook and PCKeyboardHack are not working. I guess Microsoft Keyboard driver overrules them.
Repairing permissions does not help either.
Best Answer
Two months went past, and a "legitimate" solution is nowhere to be seen. Fortunately, there is a simpler and a more radical way to solve this, and all related issues — getting rid of the crappy Microsoft drivers completely. Caps Lock, and other modifier key mappings, are easily changed in the "Keyboard" preferences. Play/Pause, Volume and Mute keys are working perfectly. All of the other media keys, and the "Zoom" slider are predictably dead, but I've never used them anyway. The "Application" or "Menu key" is mapped to ⌘ with KeyRemap4MacBook.