I had a similar issue that drove me insane, I wound up getting a second hard drive, clean install of Win10 64bit did a steam install of Skyrim which I copied the complete clean install folder to a flash drive just to avoid these issues. I started Skyrim played till I named my character. At that point I did an install of Enderal, the map was flawless. If you mod the ini file as others suggest it may work fine, I didn't find that out till I went with the clean install.
I played Enderal through including every quest I could find listed 3 times over this winters months, the only add in was the fast travel mod which worked flawless with the newer map.
If you have the room my suggestion is to do a clean install of everything, I have almost 1700 hours on Skyrim on Steam, since Skyrims introduction I probably have 3000 plus game play hours, going through a couple consoles before going to 4k on the big screen which Skyrim can not do, 1080 is best before the "level up" is perm displayed.
I wish I found this forum sooner - TIA Guys & Gals
If you need those two files I will copy and paste the data from the clean install Steam Skyrim install ini files.
I noticed the change in hard disks gave Steam cloud back up a belly ache.