I'm using dual extrusion and I am having serious issues with S3D, even with the new version 4.0.1, which claims to have solved at least the prime pillar issue. But it seems, it's not truly fixed yet, as I observed three basic problems:
1) the ooze shield is (at least most of the time) being printed AFTER the layer, rendering it totally useless. Isn't it obvious, that the ooze shield MUST always be printed first? I've read an older post that pointed this out already, but to no effect, obviously. Why?
2) the prime pillar also is not being printed before the rest in some configurations. I swapped the extruders for color1 and color2 from default right=T0, left=T1 and the result was that the prime pillar gets printed last! Since it's called a prime pillar, that's what it should do, ALWAYS.
3) I don't understand why in dual extrusion the layer numbering is different, it seems like every effective layer is split up in two "virtual" layers. Well, that alone would be ok, but unfortunately the layer numbers in the settings (e.g. used to set different temperatures at different layers) do not match anymore (e.g. layer 36 in the settings would be layer 72 in the output file). That's weird and should be corrected.
The above problems - I must say - render S3D quite useless as a slicer for dual extrusion. I will have to look for alternatives.