I did not try printing. I only checked the layer view after slicing and no matter what I set the air gap to I could not get any blank layers between the last interface layer and first layer of the object being printed. I have to assume that if it shows material in the layer view then that is what the printer is going to print. Is there nothing in the layer view that identifies the air gap layers now?
I'm sorry but your explanation and animation don't make much sense to me. It sounds like you trying to say that the printer is going to print layers under what has already been printed and I find that hard to believe.
I found the problem, which I will convey to MakersToolWorks. The problem was the extruder offset. The picture shown in the MendelMax documentation shows an offset of 33; the text shows -33. Minus 33 is correct. Once I changed from 33 to -33, we're just fine.
The 'Send' button in the 'More...' menu is for sending models to other devices associated with your MatterHackers account; not for sending to an SD card in the printer. MatterControl used to have a feature that tried to do that, but it didn't really work so it was deprecated a few versions ago.
If you want to print from an SD card, you'll need to use the Export to G-Code function and save to the SD card while it's in the computer.
The item was duplicated because you chose the instance of MatterControl which was connected to the printer, not the printer itself. Essentially, you sent the file right back to the same Queue.
In theory you should do the calibration while hot, since the length of the hot end will change very slightly due to thermal expansion. But in practice its easier to do it cold because then you don't have to deal with plastic leaking out of the nozzle.