I've encountered just this sort of thing!

After getting through the difficult parts of my build, (read: woodworking), I got the wiring/OS/MAME install done in fairly short order.
However, after making some changes to the button config with the WinIPAC utility, (not sure if I got the name of the util correct - my apologies if I didn't), I lost the use of some of my 'shift' functions as well. My IPAC was purchased new, within the last couple of months though.
I'm runnin' Windows XP and in the end, I edited the registry to run an import of the custom .ipc, (again, not sure of the name but I believe that is the proper extension), everytime I boot.
{"HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run"}
This adds all of the functions back. Worked for me. Not sure if this is entirely applicable to your situation but I hope it helps.
