Try pressing the spacebar (button 3 if you have a cabinet that has a keyboard encoder). This will take you to the rotated menus. My guess is that the left ctrl (button 1) was accidentily hit, causing the game to be listed as rotated (the -h, -r, etc on the right of the game column).
It then is no longer listed in your horizontal list.
This happens all of the time when my nephews come over to play and hit random buttons while in ArcadeOS.
<Wish mode>
If I could have one enhancement in arcadeOS is would be a "lock mode" that you can put on for parties, kids, etc. During this time, no config'ing could be done, no roms moved, etc. Just launching of games.
</Wish mode>
You would be amazed at home much a kids can change by hitting random buttons. This is why I keep a backup of my arcadeOS config files and just rewrite them if this happens