I've actually never set up the FS2 registry on this computer, and I run retail. My install consisted of directly ripping the Freespace2 directory across the network. So I don't know that what I'm about to tell you makes any sense, but it's worth a try.
Short answer, go to the Wiki and look up the SCP. You'll need it to play multi now, or if you want to give single player a go you'll find that it enhances the game drastically. And the best part, it comes with its own launcher, which sets up the registry properly for you. FS2 Retail need never have worked, and *presto* you've got a playable copy of Freespace 2.
Of course, if it's crashing because it's missing something, then that may not fix it. But it will help narrow down the options.