I think I found another solution--I had the same problem. I converted the videos using Handbrake on its normal preset, and now they run fine with both sound and video. They run best using the OMX Player. I only converted about 70 videos, but they all show the previews correctly now.
Something like this happened before with the videos from Stephen Selph's scraper, so I just thought I would try it and it worked!
Turns out the only gamelist that was created was in ~/RetroPie/roms/retropie/gamelist.xml , (there was only this single one on my whole disk, and I did search for hidden files, too).
But in the retropie_setup.sh -> tools -> scraper options, I had disabled (or forgotten to enable) that the .xmls be put in their respective rom directories.
So I deleted the single gamelist and image folder (that contained metadata for >10 systems), scraped again, since I really couldn't be bothered with manually sorting metadata for >4k Roms into different folders, and this time everything was saved to the right locations!
Thank you very much for providing me with the correct locations, the problem is solved now and the thread can be closed.
Thanks a lot mitu, it sounds pretty interesting, I will investigate it.
By the way, paradadf, I have just try skraper and It detects a lot more roms! It's incredible (and very easy to use, using the windows program). Maybe I will have to manually scrapping only few roms. Thanks a lot!