I have a similar problem with Fireworks CS5. At random intervals it will reset the preferences and choose the default keyboard shortcuts. The first I know something is wrong is when I see the "Greeting Screen" (which I usually turn off in the preferences.
However, this is not a new problem. A similar thing happened with an older Macromedia version I used to have. This is the most annoying fault. I queried this with support and they suggested an entire re-install of the CS5 suite!
In the short term, the workaround is to save any changes you make to keyboard shortcuts (I have a number for combining paths and arranging objects) into a copy of the default set. Then it's just a matter of reloading those when it happens.