I've never used the mod manager before and always just used the one the game "came with" (ever since R2, I thinkl, S2 has one as well but it seems a lot less functional).

Either way, the mod manager everyone always keeps talking about has a feature which lets you convert mods that are saved as .movie files to .mod files. The difference is that .movie files will always be loaded first while a .mod file takes its load queue order from the mod manager. Don't ask me how or why that fixed my issue but it did, so I don't really care :D

I have since uninstalled mod manager again.