I've set my Watched Threshold to 10% (from 50%). I use WMC running on Windows 8 x64 (not 8.1).
When I watch episodes in the plugin (using your very handy 'Play All Unwatched'), none of the episodes show as watched when looking at season view. The percentage is 99%, but if I 'Play All Unwatched' it always starts at the beginning.
The watched check mark on poster images used to not refresh/update on the show titles listing, seasons or episodes list until you moved to one level higher and then back into the level you want to look at.
v1.9.0 fixed this watched status check mark updating on the shows title and episode listing views.
The bug remains on the shows seasons poster view.
I can not comment on the show starting at the beginning when having a resume at 99%. I do have some epsiodes that are incorrectly listed as 1 minute long (this is the files fault not RTVHDs problem) and those do not behave correctly for the resume.