Ended up installing bestWB. Showconfig looked ok / 256 colors working.
Sysinfo still showing ECS Agnus - 2 / 68040 16.60 with IDE drive attached and 25.60 with no hard drive.
Checked and replaced gals for IDE, no difference. I wonder if the MMULIB is the one included in bestWB. In startup-sequence it says CPU checkinstall. Hopefully this is just a configuration issue.