I have been playing with a friend with the new dlc and we are noticing a lot of desyncs between the two of us that did not happen before. The end turn timer AI factions starts and ends near or directly on Clan Eshins faction flag and pops up the desync window. It seems to work after the desync for at least a turn until needing to resync again. Hope you find a fix.
We have played on Lan and online to see if anything was different and it seemed the same.
We are also playing Belegar and Durthu factions if that information helps at all.
Build Version 1.10.0