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.
Bottom line: Slic3r fails completely, MCslice works but has problems where solids cross, CuraEngine works but fails to connect some cross bars. Since I can load G code directly I will probably end up creating my own.
What makes this shape so difficult is the number of interior walls. It is essentially 60 rings held together with bars. Each ring has an interior, and all the cross bars connecting the rings create interiors. Where the bars cross each other the slicing engine has to decide what is inside and what is outside - MCslice calls the solid in between crossed bars "outside" because the surfaces cross there. So it does not print there. CuraEngine does it half the time, and the other half it simply ignores the bar altogether. It gives rows of bars and rings disconnected so the full shape is not one piece.
I've learned a lot, and I like the fact I'm pushing this technology to its limits. I know it can do what I want. It's just going to take a while. Especially since keeping the wife happy is a major factor!
I had a similar problem on my Mac. Eventually it stopped responding completely. I could still send commands using the Arduino IDE's serial monitor so I know the printer was communicating. I could also use MatterControl using another Mac.
I ended up deleting the app and deleting the contents of the MatterControl folder at '~/.local/share/MatterControl' then re-installing the current version of MatterControl. That seems to have fixed it for now. I did have to go back a re-create my customizations so if yours are extensive you may want to go back and document those before deleting.
@tellingmachine The settings for previous prints aren't accessible in MatterControl, but the .gcode files which were created to run the prints are stored in the MatterControl data folder in .../MatterControl/data/gcode. At the bottom of each .gcode file are all the slice settings used. Just line up the time and date in the History tab with the time and date on the files to find the one you want.
Here are the locations of the data folder for various operating systems:
Windows: C:\Users\%Username%\AppData\Local\MatterControl (AppData may be hidden)
Mac OS X and Linux: ~/.local/share/ (.local may be hidden)
What kind of printer do you have? I would start by adjusting the Z endstop (if you have a regular cartesian printer) or the Z height (if you have a delta). If you can't do this for some reason, then yes, you can use a negative value for the Z offset. Just be aware that some printers will not allow you to go below 0 on the Z axis. In that case, you will have no choice but to adjust the printer physically.
I noticed this same bug when running 1.4.0 on Windows 10. I don't know if there is a fix for it, but it was one of the reasons I decided to download the code and see if I can help make this great program even better.
We've seen some intermittent issues with the Mac version of MatterControl, and while we've got a new build in the works it's not reliable enough for release just yet.
As in my post on this topic on the old forum (4th from the top), you can copy the terminal text and send it to us so we can debug. If you have another operating system you can use (Windows) to use in the meantime that will probably be the best way to get you up and running the quickest.