I am having a similar issue
I am using a Microsoft Ergonomic USB keyboard and I am having the same problem. I think the issue doesn't have anything to do with the actual keyboard though.
Regardless if I use the keyboard on my MacBook Pro or I use the Micorsoft keyboard, restarting the machine often resets my settings back to the defaults. There are other times that it does this beside a full restart but I have not been able to pin point exactly when or how... I will be working and all of a sudden they keyboard shortcuts stop working correctly. Sure enough when this happens I go back to the keyboard settings and they are back to the defaults.
I would love to figure out how to get these things to stick. I ride my keyboard shortcuts like nobodies business, I have tried to get used to using the command key rather than the control key but after 15 years on a PC those things are just ingrained. I was so happy when I found out that I could switch them,,, but having to reset them every restart and several times a day is really frustrating.
