I have the same problem with the “repeat loops”. Windows 10 is my Plex DVR server, set on High Quality 30 fps, which has a wired connection to the HDHomerun extend (firmware 20170815, default mobile transcode profile). I have a very strong OTA connection to the TV station.
It appears to be a problem with the recording not the playback client. I’ve watched the recordings on iOS, Xbox One S, and ChromeOS Plex Webapp and even watched the .TS file on VLC. The Xbox and VLC each do the repeat looping you describe. Unwatchable. The iOS and ChromeOS don’t really loop, but flicker at the points where the Xbox and VLC start the loops. Annoying, but watchable.
I’m guessing you are on 20180110 (the latest as of today, and the date you posted). Sometimes the recording recovers and the looping stops. But other times it seems to corrupt the rest of the recording. It seems to be recordings longer than an hour, but I don’t know that for sure.