If they are identical batteires I'd also try swapping them around in different positions while testing the single batteries at a time.
Capactity might have also dropped causing them to report odd charge levels.
Not the same batteries, so can't swap them, but I will see if I can run with only a single one in at a time to see if I get any different results.
I had a client's X1 Carbon 5th Gen with that same issue, would think it was still plugged in when charger removed. Only fix was to do a battery reset every single time. We ended up replacing the motherboard under warranty. Do you have any warranty left on that one?
As I said above, unfortunately just out of warranty. However I did buy it used, so I'm not complaining. Just would like to have a permanent fix if there is one. If not, well...