Were you running the setup program as admin? Just right click it and "run as administrator" then change the keys to default and back again to what you like and save. Then when you run the game make sure to run that as admin as well. You can set permanent admin by right clicking the games shortcut and then going to properties, then the compatibility tab and then just tick the run as administrator box and apply changes.
This worked for me, Thanks!
If that doesn't work go into the games folder and look for the blood.cfg file(should be called something like that with .cfg on the end) Make sure to open notepad with admin and then open this file. You can then manually change the keys in that if they didn't registry with the above method.
If you do have to modify the file manually, the file name is: DUKE3D.CFG