I'm running the latest Beta. I went through and upgraded all of the Kerbal Konstructs sites that show up as ground stations to level 1. (I'm running JNSQ and a ton of other mods ... I've not had any time to do any clean testing.) Everything seemed to be working as expected.
The next time I started up the game all of those KK ground stations were back to level 0 as if I had never upgraded or configured them. That's not a terrible problem as the "default" ground stations still show up and are still working. But now I'm getting tons of NullRefs again.
I also noticed that when you mouse over the signal strength bars in the upper left (while controlling a vehicle) it shows the names of the relays it is using but the ground station that it connects to is blank, even if it's a default ground station or KSC. Not the end of the world, you can still figure it out by tracing the connection lines back on the map but I did find it interesting to know exactly where on Kerbin I was making a connection.
Logs are here: https://www.dropbox.com/s/86x4cy4jpzhciyl/KSP_logs_CJR1.zip?dl=0