Apologies for it being a while since last posting, but we haven't given up... yet.
Remembering what ProNoob135 said about how the world still didn't work in multiplayer even if all chunks were removed, I thought the solution might be to simply move all the chunks to a fresh, new world. I did this using MCEdit, for both the Overworld and End dimensions. I also copied the world icon, loot tables, structures and scoreboard.dat file from the original world to the fresh, new world using good old Windows Explorer (becuase it would take ages to recreate all the scoreboards and currently set scores manually).
Download Attempted Fix #5 here. As usual, the world doesn't have the resource pack so the link is here even though you probably don't need it.
And if it does work... please play through up to say Mission 4 or 5 and report back any problems (if any). I just want to make sure nothing broke from the copying-over before making the patch live. (If it works, that is)
I'm ProNoob's friend, just so you know. Me and him encountered a glitch on chapter 5. The gravity device is not working at all.
This seems to be happening to a lot of players for some reason... it seemed like it kept getting fixed whenever they manually teleported to the spawn chunks (use /tp @p 250 66 1000) then teleported back to Mission 5. This is something I'm definitely going to look into and fix properly for the next patch, along with removing the fake players for the team "Enemy".
I can't access hidden mission 2, tried in mission 8 and after mission 8 flying to the barriers with gm3 too, they don't get removed.
In mission 12, many of the caves dont open by defeating the dragon guys, and the i believe 4th lever in the walkthrough can't be accessed, one where the lever is at the very top of the cave thing, I think it's missing a boat or something, because I can't get higher from a place there, about half way through, I think its right above the huge arrow pointing down.