Z axis not being raised correctly during dual nozzle printing.

[akegata@gmail.com]

I installed a Chimera+ on my i3 a few days ago and have tried to get dual color printing but I'm experiencing a weird issue.
I first printed a 20mm calibration cube on nozzle 1, then on nozzle 2, both printed fine. Then I tried printing a traffic cone with both nozzles, but noticed that it looked like hotend was too low after a few layers.
I then did a print with two processes, each one printing a calibration cube, one from either nozzle. This cube on the right in the picture is the result for the cube that actually printed, with the correctly printed one on the left:

What's going on here? Is this a bug or am I somehow configuring this incorrectly?
I've attached the FFF profile as well for troubleshooting.