Seems to be fixed with 0.15.10.

Server (headless 0.15.9 on headless Ubuntu) is in Canada, clients (Win 7) are in the US. Repro steps - start server, connect with client, wait 5-10 seconds, leave game, try to reconnect, and instant desync after "catching up". After a player is first on the server they can be on for any amount of ...

! Attention !
Railways 0.4.14 is with 156 MB to huge for mods.factorio.com and i can't upload. (150 MB allowed)
so it's only aviable here atm. (sorry i don't know this before - i will try to split or remove something [again ^^] )

Have you tried optimizing your graphics? I remember a thread a ...

Edit: I resolved this removing the Bottleneck mod. I'll leave it here for anyone else who runs into this. I opened the game locally, used F5 to see what script was using the most time to process, and it was Bottleneck. I updated to the latest version from github, and it's still a very slow script ...