@Astaroth you should try and see if having russian letters in your windows username contains problems when moving the cache.ch to the new location, my friend had this problem and in the logs it spammed waiting for cache_lock to be available so he just overwrote it with -profiles=

It happens on all of the official servers, whenever they get to a later stage of the game.
When both teams go for backcapping(Getting all the zones in the back side of the warfare) the game tends to run for a long time which sometimes can be for half a day even. I'd estimate about 2-4 hours in the game is when it starts to happen.
This might just be the server not being able to handle that many assets and etc but even if this is the case there should be added extra checks to the ordering system, cause people can abuse it. The developers did not anticipate what could go wrong if the server couldn't handle it well. And if it is the server performance then i recommend cleaning out the AAF units left over from captured sectors as i have seen quite a few left overs.
Oh and if i remember correctly the 32 player servers were a little bit worse than the 64 player servers when it came to this assuming due to the AIs actually playing and using up 10 AIs each.
Sorry for late reply