Yes, if you change video cards, then you should remove the "video8.cfg" file from the games "settings" folder.
Yes, if you map the analog zoom controls the digital zoom controls will no longer function. To see if you have a mess in the key/stick settings, rename the "settings" folder and start the game. Tets without making any config changes.
If you are using stick management software, it can also mess you up if you are not careful.