It won't work because you setup the processes incorrectly. The "auto-configure extruders" drop down list is used to tell the software what extruders you will be using for the print. If you are using two extruders ALWAYS SELECT BOTH EXTRUDERS.
Their dual extrusion wizard already does this for you automatically, but it looks like you configured these processes on your own.
When I try to slice the factory file that you posted, the software even warns you that you have it setup correctly by saying the processes aren't configured to properly print with 2 extruders. Anytime you see a warning in the software, you probably did something wrong
