I had the same problem on my Iriver H10. dont know what the problem was. I have a folder in my root directory labeled videos, I could brows it and its subfolders but the .mpg files wouldent show. I fixed it by resetting rockbox settings to default.
settings >> manage settings >> reset settings.
The reconfigure your themes after you check if your videos show up.
I still dont know what caused this but thats what I did to fix it on my player.