I'd say your card or filesystem on the card is corrupted. If flashing the RetroPie image on the card doesn't solve this problems, you should get another card.
@caelthunderwing I'm using 'Reicast' on PC. Removed Reicast then updated the retropiesetup script, came from 4.2 to 4.4.1 Then I installed Reicast and updated from source, not sure that was necessary...