When I join my own server, the progress my (and other) characters have done rolls back. I have tried restarting it. It's not really a big deal since I'm on creative and I can just respawn my stuff, but it seems that my player.dat file just doesn't change at all.

I honestly don't know how to replicate this and the server has a good amount of command blocks, so if you want I'll give you the IP and you can check it out for yourself or I'll send you the map.