Using Windows 7 HP 64-bit and installed the game through GOG Galaxy in a custom G:/ directory. Also installed the HD mod and it runs fine through it, however I'd like to be able to play vanilla as well....

Any ideas?

EDIT: Did a clean boot and it works fine, now I have to fish for whichever startup program is preventing it from launching....

Now that I've started playing I'm noticing low frame rates, around 12fps... Is this normal for everyone?

You sure you configured the game speed in the game's options?

Yes, I fiddled with the speed settings. I also fiddled with the stretch filter in the HD Mod launcher at two or three of the options actually seem to help considerably (30+ fps).