Ok can we start with the Megadrive.. indeed the Megadrive shouldn’t really cause issues, other than maybe a little vertical trembling.
Can I get your model of Megadrive (1,2,motherboard revision if you know it) and your exact cable type (you say CSYNC, but who produced it and is it wired correctly?)
On the Amiga, I have a CD32 here (with SX32) and have no colour issues, can you maybe show a screenshot of this?
AES seems to have some issues for some folks, maybe I’ll get one for myself and try at some point (I wonder what the tax man would say to a business expense of a AES console 🙂 )
Connecting via AV3/VGA DOES help with some systems so if you can try that, that would be great. This is a known bug Markus is working on. Remember to turn DDSP on your Extron interface to ON.