It's a known problem. AmiCygnix uses 16-bit screenmodes, but expects a big-endian 16-bit mode. However, Southern Islands GPUs (like the R7 250X) don't support big-endian 16-bit textures. So, 16-bit modes are little-endian. Since AmiCygnix assumes that it has a big-endian mode all the colours are wrong.
AFAIK the Amicygnix author has been informed, so hopefully we'll see an update that addresses this problem.
Hans
That probably explains both
this, and why I had graphical issues with Freespace in software mode.