Mods have a nasty habit of screwing the game up. If you're going to use mods, you simply have to be prepared to have your game do funny things. Do you use Fallout Mod Manager?
It's likely to be mods causing it, but if you don't know for sure go through the ending with all mods disabled. If it works fine, then I guess you can then go through the ending over and over, disabling a mod one by one til you figure out which one it is.
If you don't want to do that, stop using mods, or stop finishing the game, or just carry on disabling them just before you finish. FOMM makes it all a bit easier, so if you don't have that I suggest getting it.