A hot end may smoke after servicing/ cleaning when using any cleaning fluid, grease, sweat from fingers or excess residue. I do not think that it is any cause for concern. Continue to feed filament out of the hot end and if the problem persists, open up a support ticket.
This usually infers that the x-axis limit switch is not working correctly. I saw in the video where you were tripping the the switch by hand and measuring with the multimeter, but there may be a loose connection somewhere at the switch or on the board. Another possibility is that the wiring is frayed, thereby making the signal intermittent. If nothing seems to work, go ahead and replace the switch with a newer component and see if this makes a difference.
My thoughts are that the settings are not completely correct and that the filament looks wet. I assume that you are printing with PLA. I need to know the hot end temperature, the bed temperature, the type of surface to which you are printing, adhesives, cooling fans enabled/disabled and slicer being used. If you want to discuss specifics, please drop me a note at email@example.com. In general
home z with the probe being usually a ziptie thickness higher then hotend tip. if use marlin firmware m211 s0 to disable soft stop and m211 s1 to turn back on when finished. this is the software stop protection to ensure you do not go below z 0.0 then use your display knob to move z down 0.1 at a time till you just grab a standard office paper look at display and check z (EX:-0.5) that is how much you set z offset for you can do that with (m851 z[your offset amount] + thickness of paper for office standard usually 0.1 so if was -0.5 your z offset is 0.6 (Ex: m851 z-0.6) then a m500 to save to eprom m501 to load eprom and reset do a test print if its to close or to far adjust by 0.1 (Ex:m851 z-0.8) then save reload
if using a different firmware im sure it has a similar no -z protection that needs to be temp disabled.
Tried Installing on RPi3 with Ubuntu Mate 16.04 as it is implied in the "Development/Running on Linux" page to be operational. MatterControl still won't launch after going through all the installs of auxiliary packages. It just hangs and locks up the RPi, cursor still moves but nothing is functional. Had to shut down through SSH.
Any kind of direction would be greatly appreciated.
Update 1/9/2018 Problem persists was printing perfect at 1.5 for last 2 days then started printing to high had to bump to 1.7 :/ not sure i checked everything from probe to lead screws nothing seams to move and is tight. if wasnt for this one issue i could hit print and walk away when it stays every print is spot on then just changes.
Sorry, its not setup to work on Linux. It's looking for avrdude.exe as if it were on Windows. I'll file a bug report. In the meantime, you should be able to make it work by installing avrdude as you normally would on your distribution, then make a symlink from /usr/bin/avrdude to /usr/lib/mattercontrol/avrdude.exe.