You play a file, then you stop it, then you start playing again and WDTV asks you if you want to resume where you left off your start from the beginning.
Due to the cut-off-time being exactly after three hours, this sounds more like a timer somewhere (wdtv, tv, …) kicking in than an issue with a file, especially, when the three-hour-cutoff is also happening when starting anywhere in the file.
I tried remuxing but that didn’t help and I was trying to avoid downgrading to an earlier firmware which is what a WD technician suggested to me to do but when I saw what I had to do, it’s too complicated because originally I got an IT technician 2 set it all up.