I need to do some more testing on some fresh missions but yes it does use an .init and I have the jebus scripts in the mission folder.
I think F3 is somehow hijacking the init because not only does jebus not load, but that little loop to hide the markers (1-100) from UPS does not work either.
EDIT: I tried it with a vanilla F3 mission and added a squad of ai with default jebus and it worked! So disregard, it must be some settings I have messed up