I have this issue as well. Programs that I know I haven't watched show as watched already?!? I thought I was losing my mind at first
I think you're correct in that it is only those that would have been recorded during the viewing of another program, so your though of them being in the PiP buffer would make sense.
DIRT is looking for people having the 100% watched problem.
go to
http://www.satelliteguys.us/threads/330165-UPDATED-DISH-Needs-Help-from-Hopper-Users!