I see, I'll give the SNES sync a test the next time that I have the TG setup for testing. Thanks for the suggestion.
It can't be the 480i issue because the GBS works with SNES, Genesis, Amigas, N64, Saturn, as well as with arcade boards (MVS, AES, etc). All of these systems output 240p. It interprets them as 480i, which is problematic, but they are all able to be converted relatively well.