The wiki says “Games running on this PCB use 240p with odd field signal modes. To ensure the game works correctly, select the correct input on the OSSC before starting up the game and do not change it during game play.”
Hardware like this has caused quite a number of headaches it seems. You could try connecting another source to a different input and switching to that then back to the F3. A bit of a kludge workaround but it has worked for me in the past.