While messing around in the retropie settings menus, I realized opening the 'retroarch' settings would trigger the hdmi logo. None of the other menus. This lead me to believe retroarch was doing something with resolutions etc. Turns out disabling the fullscreen mode stopped the annoying little hdmi banner. Confirmed by entering and exiting the retroarch settings menu from the retropie settings. But that doesn't exactly apply when I actually try using lr-mame. It forces the fullscreen, even though it was saved.
Everything was default when I started having these issues, guess I'll just try a fresh image.