I also wanted to disable the splash screen and in my case I ssh'd to the machine, remounted the root partition (https://wiki.recalbox.com/en/tutorials/system/access/remount-partition-with-write-access) and disabled the related init script :

# mount -o remount,rw /
# chmod -x /etc/init.d/S06splash

Inspecting the script there seems to also be possible to create the file /overlay/.configs/skipvideosplash to skip the videos, but you should write-protect this file, because it would be erased after the first boot.

I have similar problems:
sometimes, music in Emulation Station stops working. When this happens, the next game that I try to start freezes with a black screen showing only the navigation buttons from emulation station at the bottom.
Rebooting from recalbox manager usually fixes the problem.