After a few hours, we figured out that RailPowerSystem is the one mod desyncing him upon joining. In one test, we disabled the mod, saved the map (removing all of the Rails), re-enabled the mod and he was able to join with no problem. I took a screenshot of the Entity count upon disabling the mod (with all of my other mods enabled). Here's the amount of Entities that were removed: https://i.imgur.com/PsaaCea.jpg
Hopefully this can get fixed soon. Would rather not remove most of my Rails... Especially seeing as I converted all of my vanilla rails over, too.