I say there's a conflict between the 2 installations. Try renaming your vanilla install to Silent Hunter 3 Vanilla. Do you have SH3 Commander installed? That needs the path set to your GWX 3.0
Vanilla SH3 is just the basic broken sim that we had to play until the patches came out and them the mods to "fix" the game. Most everyone will tell you to just keep the vanilla as a backup install, and play GWX or one of the other mega mods. You'll enjoy SH3 even more.