I just took a guess at it & got the result you mentioned: It happens, for example, when a series has the same ShowID for all the episodes. So, when you mark one episode as watched, then return to the main list, SageTV then sees the entire list as watched... until you refresh the list by scrolling the main list by a page up/down & then returning. The watched show then gets sent to the bottom of the sub-list & the category title is no longer shown as watched. That's one reason why you see it as intermittent.
Edit: Correction. Having the same ShowID had nothing to do with it! Oops.

It does it with any list of shows -- simply set the first show in the sub-list as watched. As long as that does not cause the main recording list to become reordered, the category will now be displayed as watched. It looks like the category's 'watched' setting depends on watched shows being sent to the end of the sub-list; therefore, if the first show is watched, they all must be. Unfortunately, the sub-list isn't reordered immediately, causing the result Watter reported.
- Andy