From what I understand, this issue has to do with armor stands having their chunks loaded and unloaded which sometimes causes them to completely lose their scoreboard values. This was an issue for me when I was making the main menu, as a certain area of the tutorial was just far enough that it caused the armor stands to quit working. I have no idea why this issue happens, I can only take measures to fix it (i.e. re-assign every scoreboard value to the entity). Luckily for me, they can't lose their NBT data (like their name) so I can always identify them (this is the reason "Node Repair" works).
I'll try and work up a solution to the checkpoint problem. It should be an easy fix, but it might be hard to test since I pretty much never run into this problem myself.
This bug is now fixed. Hurrah!
Congratulations on fixing that bug, @Flamingosaurus!
I'd probably experience those bugs if I played the map enough. By the way, I think I've been playing this map on October, and the map is great!!
Keep up the great work, man. I'd love to see more updates to this awesome map. By far one of the greatest maps I have EVER played in my life. Not only that, but it also looks like a 1.7 map, but it's not. (That's a good thing), and also, I think I've been playing Minecraft since 2011 or 2012! So again, this is one of my favorite maps EVER on Minecraft!
EDIT: I know I just got an account for MinecraftForum, though.