I have noticed this also and it is very annoying. After updating the retropie setup script the randomizer is disabled and needs to be enabled after each update...
@capninja You're now dropped to a shell where you can execute commands as root. The # is the command line shell prompt. The usb keyboard problem could be because the USB drivers are not initialized in safe-mode.
I think that the safest option is to re-install. There's too much fiddling with the CLI and it will be safer. Even if you managed to recover the sudo functionality, there's a high chance something else is broken and normal operations would not work.
Just on idea on the splash screen set-up: right now if the system has a launching.[png|jpg] in the /opt/retropie/config/$system folder, it's shown as splash screen. Can we add also the /home/pi/RetroPie/roms/$system as search path for the launching.[png|jpg] file ? This way copying the ROM folder would copy the launch image and it would make it easier to transfer/backup the launching image ? It can also be something like /home/pi/RetroPie/roms/$system/images/launching or /home/pi/RetroPie/roms/$system/media/launching (which I'd prefer, since scrapers can save information in the media folder).
@phanhuyen unfortunately the new version doesn't run well. Since we install the Debian packages, it's possible the Stretch one doesn't also if it's been updated. New version on SDL2 uses opengl afair from my testing and is slow without.