As Basil noted, Roku has very limited codec support, as well as the container the video is in. If you stick with H.264/MP4 video and container, with AAC audio, it should always work. In my experience Roku still has some issues with some H.265 content, but I haven't tested it extensively. Also, I don't use the USB port, but instead stream from my DLNA server on my home network. I let the server transcode files that normally won't play, so I don't have to fiddle with Handbrake. It's a great product, but offers so much control it's easy to get lost in the settings.
Dan
Roku Stick (3600), Ultra (4640), 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.