I'm liking the updates so far, but I have one issue that is more cosmetic than anything. It has to do with the "show queue preview". The red line that used to trace vectors in the Polargraph 2015-11-10 version of the controller now has issues in the now current version of the controller in Polargraph 2016-01-24. The red line does not trace the vectors, but instead only moves in the X direction and likes to hang around the top right corner of the machine size box.
Another thing that I noticed is that the queue length is about twice as long now. I haven't tested it yet to see if there was any difference but just wanted to bring it up.

(The older controller is in front of the updated one.)

Re queue length, try changing the "shortest vector" option - it isn't normally 0, and shouldn't really be (might end up with lots of single-point paths).