If Vogatek Supergun is outputting TTL sync direct to the OSSC that may be the cause of the damage, especially at higher voltages (JAMMA video spec is all over the place). Damage caused by that wouldn’t be covered in the warranty unfortunately. However I can’t be 100% sure that’s the case. There were reports (from SuperG with his GScart) of people using similar Superguns with this issue and that causing his units to stop working.
Could you open your JAMMA SCART cable and show a picture of the wiring perhaps?