Hello Steve! I do not follow, are you marking it watched in SeriesGuide or using another app or service? E.g. if they are connected to Trakt and changes do not sync to SeriesGuide, you can try to disconnect and connect Trakt.
I am using Series Guide to watch various shows in CyberFlix and when the show is done (all the way to the end) Series Guide is not automatically marking it as watched as it has done in the past.
I have to go up to the watched check mark and click on it to show it as marked and go on to the next episode in the series.
There is no automation that would allow other apps to mark an episode watched in SeriesGuide.
Looking at the description of Cyberflix it is integrated with Trakt.tv. So check if it is still connected. Also for SeriesGuide make sure to not use SeriesGuide Cloud and only Trakt.