I just started playing with boot logos today, and I saw something like you said. After the logo is uploaded, the player reboots, the boot animation runs, but towards the end, the POST and animation flicker back and forth for a few frames. This only happened once I uploaded a new boot logo. If I unplugged the empeg and then powered it back up, the flickering is gone and everything works as normal. I am not worried as rebooting after the upload fixes this for me.