Found the problem with my 3D MVC files, the Stereoscopy flag in the problem MKV files weren’t set to 13 (or anything). These files worked fine in RPi Libreelec as that uses the filename. When the flag is set to 13 they work correctly on the Vero.
Thanks to this post https://discourse.osmc.tv/t/3d-frame-packed-output/81681/61