Do you have Suitcase font management?
I did already replace the preference files.
It was actually happening on multiple InDesign installs on separate computers so I don't think it could have been preference related.
However, crossing my fingers, I think it is fixed now...
I created a copy of the original document and exported the .INDD document as a .IDML and re-opened/saved it as a new version. By doing this, everything appears to be working now. Don't know if it is just coincidence or if something in that process really fixed something. I guess only time will tell.