I had the same kind of issue with my SNES Jr/SFC Jr despite correct soldering points on console board and the same Retro Gaming Cable NTSC SCART cable as yours with the Nintendo RGB Bypass Amp Revision 4.1b by VGP.
I remember I had to solder jumpers J2 (Change Csync Attenuation) and J3 (Buffered Csync) to sync picture properly. Since done, it works like a charm with a perfect sync and crisp RGB signal on my CRT (via SCART) as well as an upscaler (successfully tested on OSSC and RetroTink 5X).
I hope it’ll help you.