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.
Well I figured it out - very much self-induced. The PTFE tube in my e3d was pushed up ever so slightly and I was getting some melted filament in the heatsink. This was causing a lot of backpressure on the extruder (Bowden) and reducing the flow. There was a plastic tab missing from the collect which I think fell to the bottom of the hot end and created the gap at the end of thePTFE tube. Some prints had obvious under extrusion, while some were okay. Talk about hard to diagnose!
So I think the differences between slicers is the fact the Slic3r defaults to 200% extrusion width, while MC uses 100%. On small prints that "fixed" the fill issues when using Slic3r. Since the models were most low fill the walls looked decent on both, even with the higer backpressure. On larger models not as well but stil better. Now I'm happily back to using MC and getting great prints.
The info about the files for review is nice to know. I've already used it to see what settings I previously used to print a piece. Wish there was automatically reuse that data as long as the part stays in the queue. That'd be icing on the cake but just having the settings recorded is nice.
I don't always use mattercontrol to print though. Usually I use it to create the gcode, then upload it to a laptop I have running OctoPrint. If I create the gcode with repetier the bed will heat first, then when it gets to temp the hot end will turn on. That's what I'm trying to replicate with mattercontrol.
I think I have seen this before on a Fedora system. I suspect it might be graphics driver related (that system was an old Nvidia card with the Noveau driver). What graphics card do you have and which driver are you using?
Also, it probably wouldn't hurt to make sure you are on the latest Mono. We test on version 4.2.
MatterControl 1.5 has been released, which has built in profiles for the Makerbot 5th gen printers along with the ability to export X3G files, which you can print from the SD card. You still cannot connect directly to the printer over USB, but we are working on that and it is one of our top priorities at the moment.