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.
Sorry. We tried to replicate your issue using our Flashforge Creator Pro, but we were not able to do it. Maybe there is some difference between the Flashforge and the CTC that we are not aware of. Without having one here for testing, there is not much we can do.
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.
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.