When this happens, I usually end up killing SONAR (taskkill /f /im sonarplt.exe at an admin command prompt) and then just unplug the FaderPort before restarting. Unfortunately, SONAR's handling of restoring device settings seems to be essentially random so then I have to dig back through the settings and make sure the FaderPort MIDI and control surface ports are correct.
In my experience, this seems to mostly be associated with missing plug-ins. For example, I have my Waves licenses on a USB stick that I move back and forth between my main system and a laptop and basically can't open projects with Waves plug-ins without going through FaderPort hell if I forget the USB stick. Something with SONAR's control surface initialization code seems to conflict with the plug-in loading code which causes it to get stuck on startup. It seems most likely to happen if I'm missing a plug-in or a license or have an expired eval license (not uncommon scenarios) but I'm pretty sure it has happened to me without this.
Another issue I've had from time to time is that the FaderPort motor stops working. Changing tracks causes it to assign its current position to the newly selected track's level instead of moving to represent that track's level. The only way to solve this that I've found is to rerun the firmware installer. My guess is that the FaderPort has some sort of onboard memory that gets corrupted and the firmware installer resets that.
Pretty frustrating that a device that is supposed to make life easier ends up resulting in so much time and frustration :(