Not compatible with nightly version of kicad
It seems in the nightly version of kicad the layers are defined with quotes in the kicad_pcb file.
Eg, "Edge.Cuts" opposed to just Edge.Cuts and "Eco1.User" opposed to just Eco1.User
I believe this is breaking functionality in the panelizer.
If I manually replace all instances of "Edge.Cuts" with Edge.Cuts and "Eco1.User" with Eco1.User in the file then the tool behaves as expected.
Not a big deal, but FYI.