Alright, I finally had a chance to go through this and I've noticed that you appear to have vp files in the data folder. I can't remember if we said we'd just update the main folders or have each campaign in its own folder. But VPs in the main data folder is definitely wrong. Ideally, the only files that should be there are the movies and Freddocs.
Also if anything replaces an existing file, it should replace it (unlike the ships.tbl which is in data). Does that file have priority now? To be honest, I don't know.