If you have frame rate matching enabled, try turning it off. For me it's always messed up MPEG-2 playback. Works fine with H.264/265 or MP4.
I haven't tested frame rate matching with the released version of 9.3, but it was still a problem with earlier beta versions.
Dan Roku Stick (3600), Ultra (4640), Ultra (4670), Ultra (4800), Premiere (3920), Insignia 720p Roku TV, Sharp 4K Roku TV, Nvidia Shield, Windows 10 Pro x64 running Serviio and Plex on a wired Gigabit network.