I'd say this needs to be moved to the mods section. The developers aren't responsible for the fact the game may not work as you want, when using a mod to bypass the design of the game.
As to your problem...since I don't know the mod you're using, I don't know what it's supposed to do beyond let you FT out and continue play. Is it supposed to let you continue quests, or just continue running around killing? Name of mod?
after the final battle the main quest is completed and you're sent to the ending movie screen, the credits scroll, and you're sent to the main menu, this mod simply turns that ending movie into a room with a projector showing the movie and an NPC in the background to product the narration voice,after it stops you're allowed to get up walk around and fast travel back to the wasteland, it doesn't change any quests or anything like that, it just changes where you go for the ending so you aren't locked out. so i don't think it would have an effect on the quests(i've completed several after using it) here's the mod: http://www.newvegasnexus.com/downloads/file.php?id=39304