While dual printing, Cura will print 2 layers each tool change vs 1 layer per tool.
Slic3r will switch back to the other tool at the layer change
Here are some pictures of the artifact in question which only occurs while 2 extruders are in use
Here is the same model sliced in Slic3r and printed on the same machine
My hypothesis is that perhaps a layer time that is too short isn't allowing the material below the new layer to cool enough before another layer is applied. My reasoning for this is Slic3r's way of doing it allows more time for the layer to cool before another layer is applied by switching to the other tool/part before applying the next layer.
Another theory I have heard from @kent is that the backlash isn't being compensated for properly when z move occurs without a tool change. He may be able to explain that better.
Perhaps applying this change would mean more frequent tool changes and/or an increase in print time, and may shorten the life of the actuators on quiver.