It seems pretty clear to me that this is a doubling of the Video Output FX. That's why an Invert FX negates itself, or why color FX get twice as strong.
This is what I've added to the known issues post:
"[VP17+] The effect of Video Output FX is doubled during Warp Flow transitions."
If anyone disagrees with that, please let me know.
While that's nice to know, it's unfortunate that the fix to the bug requires another expensive purchase. Wish they had fixed it for the people who still own VP17.