So I didn't update mbincompiler for a while. Was using build 1.0.128 for ages cause it worked.
Decided to update and noticed that the game was crashing when I had edited ROOT.MBIN, even though I didn't make ANY changes. This has happened before though.
Here's a comparison of the 2 ROOT.MBIN's, the left one is un-compiled rip straight from the .pak, the right one is simply ROOT.MBIN, not edited, but recompiled with MBINCompiler.

ROOT-NEW.MBIN has 16 bytes missing from it.
ROOT-NEW.MBIN crashes the game on loading screen, when using MBINCompiler build 1.0.164 but works fine with build 1.0.128