Well that's good to hear. There is a tool to clean the registry. I have it linked in the FAQ of Bootleg, and I intend to put it here as well when I get around to that section. I always use that tool + CCleaner when I want to start with a "fresh" install. During my testing this summer, I had to uninstall and reinstall back and forth to each version of the game, and I know a few issues popped up early on when I didn't clean the registry between those installations.
Insight has worked on a new version of Bootleg for us, so it's possible he's run into the same situation.
DrLilo used one of the movie mods as a base, but you will definitely notice the difference once you get to a scene where the character models are being animated in front of them. He removed all the old, blocky Chibi models and them replaced with Kaldarasha models. For any scenes without the models, I just added Rumbah's Smooth to complete the pack.
When you get around to installing Gameplay - Difficulty and Story, be sure to move it to the top of the list. I have no issues so far when it's loaded first (keep in mind, I haven't tested all of them in a full playthrough...that's impossible for one person lol).