This is something we have seen before. The fix is already in the code and will be available in the next release (1.6). If you need to use it now, you can download the experimental version. Beware, though many other things are broken in the experimental release.
>Your other issue with the print leveling moving the Z axis instead of
the Y axis is strange. Does it do this as well when you move the Z axis
through the regular movement controls (i.e. not through the print
Nope, everything works well outside the leveling wizard. Except the z platform height.
On Arch based distros make sure you have installed mattercontrol-plugins as well. This has the closed source plugins including the S3G driver for Flashforge printers. Also make sure you have given your user permissions for the serial port. See the wiki article on running on Linux.
What exactly is wrong with the default start gcode and what are you trying to change it to? We've done extensive testing with our own Flashforge and it works fine.
Why are you trying to change the config file instead of editing the start gcode from within MatterControl itself? The settings in /usr/lib/MatterControl/StaticData/PrinterSettings/ are the default settings loaded when you add a new printer. Your own settings are stored in an SQLite database in ~/.local/share/MatterControl/ (in 1.6 these will be moved to .json files)
Slic3r and Cura engines are disabled for dual extrusion printers, since MatterControl currently does not support dual extrusion using those engines. I realize its a little confusing to have them completely hidden in the menu. If you want to try Slic3r anyways, switch your extruder count to 1.
For the Flashforge issue, could you post your slice settings and your old/new X3G files for comparison? In fact, if you could export a gcode file and post that too it would probably be helpful.
As for the Robo, could you tell me a little more about how it freaks out? It sounds like maybe some issue with your Z axis stepper motors. Does it move up and down all right when you use the manual controls?
Besides telling MatterControl is was a MakerBot Replicator 2 printer what other settings did you change from looking at the Maker Architect manual? I have heard people say this but no one elaborates on what the settings from the manual are. I have this exact printer and I am running into some issues with it not using the whole print bed and some stuff being to small in size. Any help on getting the settings down right would be much appreciated.