On the UM2 you have to compensate the 20mm retract of the material change wizard.
Make some calculations and increase the "Retraction amount" for the pause at height plugin (it's in cubic mm if you use the UltiGCode flavor).
Re-sclice and you'll see the difference....
I had that problem once also, it seems to me that after changing material the filament is retracted. I'm not sure if the latest firmware update corrects this but here's what i do now:
After the change material and before resuming the print, i hold the pressure lever of the feeder and push the filament by hand to be sure that it's extruding, then i resume the print...
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