+1 here. Just happened to me this morning. Throwing in my details.
No, I've relaunched the game multiple times since the last patch that went out. This did occur after a re-launch though.
Only 1 Active run - on a "ng+" Level 2 prestige run on Sal that I started immediately after completing the story for the first time.
Since this issue:
The new run appeared to persist but I didn't play it long enough and abandoned the run.
Yes, the abandoned run shows up.
Doesn't seem like it. The end turn option was not disabled, which was my preference.
Here's also a new wrinkle - my internet went out last night so my save didn't get uploaded to the cloud this morning. I manually redownloaded last night's save and the issue was already present. (Unfortunately!) I do remember during the last few encounters in my story ending run that it was already not remembering the end turn option and the pop up saying it saved my preference kept happening.