I have had similar issues with S3D and my UM3. Same issue on prime line. Very little extrusion on additions -- skirt, ooze shield, prime tower -- but the print itself extruded well. I had to turn those features off because they caused more problems than they solved. I needed them, but couldn't use them.
In two other seemingly unrelated posts, I questioned whether the additions used the same first layer parameters, and I also bemoaned S3D's confusing manner of handling dual extrusion.
In figuring things out, I ungrouped the processes that were grouped by the dual-extrusion wizard. I found that the additions now printed fine. There were two ooze shields, however, that tried to occupy the same space. I regrouped the processes and only had one ooze shield and finally got some great two color prints.
So now I ignore the dual-extrsion wizard and just create and edit two processes. I only group them when I am done editing each independently, and only if I need an ooze shield. Unrelated, but I also lessen ooze by lowering the temperature of the idle extruder by editing the gcode script for tool changes.
This did nothing for the collision of the priming lines, but that didn't seem to cause any issues.