After starting the game after loading 1.3 my factions are all screwed up.

The Arcean mod caused the game to crash when I tried to play as the Arceans, so I removed the Arceans from my mods.

When I restarted the game the player selection was blank and when I tried to select a faction to play, I was getting a random faction instead of the selected faction.

I finally gave up and uninstalled and reinstalled the game.

When I started the game the player selection was still blank, so I moved the Arcean mod back into my mod files and after restarting, I was able to make a player selection.

Then I noticed that all my mod factions (i.e. Gauntlet) were showing up, but all the steam factions that I have subscribed to have disappeared. When I check with the steam workshop they show that I am still subscribed. 

I tried unsubscribing and resubscribing a faction but the faction did not load when I restarted.

I am never sure when things like this happen, if the problem is steam or GCIII. I have had ongoing problems with the ship design part of the workshop. After submitting tickets to SD and Steam with no success, it turns out that the problem is intermittent connectivity. You can try to upload a ship design and it rejects the upload with no explanation. One second later or two days later, it works fine.

I have done the refresh procedure with Steam which is about all you can do with that app. If anyone has had a similar problems or has any advice let me know