It works for the most part, but when I pause the game to do save glitches (especially for the part where you have to find 4 boxes) it rarely works and sometimes it just starts randomly in the menu. Any way to fix this? (I used this tutorial:

Are you saying that the timer isn't pausing when you pause the game? If so, this is a known bug with the autosplitter/load remover on new patch, the moderators will retime your run, but if this something that is really bugging you I suggest downpatching to old patch.

I downpatched it and now it works (almost) perfectly