There's a note on the dev wiki.
"The first color of the palette bank ($400000) is the Reference color for the video output. It always has to be pure black ($8000) otherwise monitors won't be happy and other colors won't be displayed correctly."

Not sure how this affects the sync.

On viewing via Kawak's Tile Viewer, the 1st colour does appear black, but on reading directly from the ROM, it showed that it wasn't. Setting it to black solved the bulk of the problem.