MUI 3.9 and 4.0 colour problems.... yes, currently it was linked to VisuaPrefs pens prefs (bummer) Hopping to have a solution soon, because it's really annoying.
And yes AmiKIT 8 has a big bug with default colours, where draw pen = background in MUI and something else I have spotted. Disappointing, and sadly no online update/quick fix is provided. (for lazy people)
Have not tried 68k MUI 4.0 on the real amy yet, but I guess it should work similar to OS4 version, and I am not happy with that either at the moment (the way the colour are handled, since legacy MWB support is somewhat broken, and
I love XEN style, that has been removed a few month ago