Famtasia isn't great, there are a number of reason one would want to avoid it when making an encode.
But if it doesn't sync on anything else you might be stuck.
I have a possible work-around, but I don't know what kind of practical limits it runs into.
If the movie syncs on famtasia and the savestate data for each frame could be recorded, could that then be played back with TASEditor?
IE a large collection of single-frame from-savestate movies, using famtasia to recreate its faulty logic and something else to render the A/V.
Edit:
ACK, the famtasia source code is lost, pulling the savestates out of the .exe is probably nigh impossible.
Oh well, plenty of SNES youtubes to encode.