Alright, we've figured out what is wrong.
A scripts build that was released (we aren't sure which, and at this point, I don't care) set all the vehicles to type "turret". What this does is tell the netcode to treat them like turrets, which usually do not move, so vehicles when they moved became desynced as the netcode is not designed to handle moving turrets. This was an easy fix however, and all vehicles are once again set to their respective (correct!) types.
It's going to take a bit to release a new version however, so I've gone ahead and added a few bonus things. Ion Storms will come back, using brand new scripts that make them easy to place in maps, so for example Timeaua's maps could implement them when the patch is ready and it would take him about 2 seconds to implement, compared to previously where a lot of hacky stuff had to be done. They will only affect Radar for now however pending a lengthy discussion on how they fit into the game. So basically they are purely cosmetic until that time.