You have to match the settings of the two video sources so that they are the same in frequency and phase, both vertical and horizontal. Since I don't know what your two sources are, I can't help you except to offer suggestions.
The U-Boot screen is a VESA standard, 800x600. I don't know what scan rates it uses, I've never measured them. You will have to change the settings of the test screen shown so that it generates the same rates. I suggested one change, but you will have to experiment until you get it right.
Sadly, no one uses Genlocks these days. They went out of fashion with analogue televison a couple of decades ago.