So I had this issue with games running in 240p or 480i switching randomly between the resolutions, not so much of an issue with DVDO alone but with OSSC the transitions are not as smooth. They will often break recordings, desync the music, cause your TV a heart attack ect.
Enabling unlocked framerate in DVDO fixes this partially, the recordings no longer break nor are there any de syncs or TV acting funny. You still get the blue screen of no signal for a moment but that probably cant be helped with OSSC at least they're fairly short and they dont cause any damage to the hardware.
Here I had it set to 480i passthrough and 240pX3