Guess I’m not the only one having this issue. Same thing happening with video splashscreens on both my RPi 2 and 3, both running clean installs of latest Retropie 3.6.
The first reboot after selecting a custom video splashscreen, the video shows, and then perhaps it shows on the second/third reboot too (I wiped SD and reinstalled a few times) but without fail on subsequent reboots there will be no video. Yes, I get that same pause too and can tell that the video will fail to play.
If you turn of autostart of emulationstation and turn it back on, sometimes on reboot you get video splashscreen back and then on subsequent reboots no more video. You can also temporarily get video back if you disable fastboot but it doesn’t stick.
I have no idea how to fix this, so gave up and went with a custom static splashscreen instead of video.
I don’t see anyone else posting about this besides 2 other guys in this thread;