after continuous testing I found the reason for the timing problems: Indeed it´s as i thought!
The two FPGA’s are the problem. If i put my retrotink 2x pro in passthrough mode the timing probs are gone.
The pic is clear and crisp and everything ist working as expected. Exept the pic format. Now i have a widescreen format on my LCD Screen instead of the requested 4:3. But this is a problem of my display. Everything would be perfect if i could force it to 4:3 …