Lookyng at your configuration I see was a normal one so there should be no software conflict involved I guess. Maybe D+ log could have provided an hint about the issue 
Files in my pending list are added to track file modification occurring when you use install or trusted policies. It also track deleted files (to know if something important was deleted).
So as long as some file will be changed youâll have to move it again to the safe list.
if you purged those entries before moving then that was a bug