Thanks for the support Mavis. The issue seems to be gone.
However, Now every time I open onenote I get a "We're sorry. OneNote is cleaning up from the last time it was open"
The only time I've really seen this happen is in conjunction with the ink disappearing issue (This one, and also the old one with the pre-release windows 10)
So I'm thinking either I need to clear some cache somewhere, or you fixed the result of the problem (the disappearing ink), but not the cause (which also causes the cleanup message I'm getting, and the flashing issue that's also reported on this thread)
Do you have any suggestions on what I can do to fix this?
UPDATE:
It's more sporadic than I thought.
Actually this issue seems to appear if close onenote and reopen it quickly afterward. If I wait a while, the issue doesn't seem to show up. I'll keep watching to see if I notice anything else.
While I would prefer to never see that message, I can live with this. Now I'm thinking the "issue" I saw earlier was just the expected behavior that I ran into because I was trying to quickly close and reopen OneNote to fix the disappearing ink issue.