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I’m not using the same configuration for a controller for my MPCNC. I’m using an Ardunio UNO with a CNC shield and GRBL v0.9. But in principle I think you should be able to try the following:
You should NOT need to reflash your Arduino with Marlin as you are doing. That is not normal. If you are certain that you need to reload Marlin in order to correct this then you need to see if you can isolate exactly what is happening. Is it that configurations in Marlin are getting changed when you run the job. If so is Marlin somehow doing that?
Before we get started, have you tried any other gcode other than the one example? I did my testing by creating some gcode that drew a 100mm square, then a 100mm diameter circle with its center at the center of the square. Later I added some additional shapes, all aimed at verifying that things were aligned properly.
I haven’t looked at the gcode for the example you are using and I expect it is fine, but I had copied some torture test code from another thread here and it was missing the “F” from the Feed rate values in several places. That was interesting since it was trying to goto Z-30650 instead of Z-30 at F650 or whatever the specific values were. I just mention it since starting with a very simple “hello world” sample might eliminate any chance that something about the gcode is causing problems. That said there’s not too many things that you can do in gcode that would stick beyond the running of the gcode, but there are a few things. So maybe worth a try.
So let’s try some steps to isolate the problem..
1 – Run your successful test.
2 – Now, using Repetier’s command line entry box try sending some gcode commands to the MPCNC. Just some simple stuff to start, move to different X and Y locations, different Z heights, etc. There are good references on line if you are not familiar with gcode. It’s pretty easy for the simple stuff.
3 – If there is a problem then you need to dump the settings from your controller firmware and see if any of the things like number of steps, max feed rates, etc. have changed. If the settings have changed then you need to reset them. If you don’t know what they are reflash again, and capture the values before you run the job.
4 – If none of the controller configuration parameters have changed and there is a problem with manual commands then try closing the connection to your MPCNC in Repetier, power off the steppers, power cycle the Arduino controller, power back up your steppers as usual. Then re-connect from Repetier and retest.
5 – If this test works then something is happening with your controller that requires it to be reset between jobs. Someone who is using the same HW / Firmware setup that you have may have some specific suggestions on that.
6 – If that test did not work there is one other thing you could try. With GRBL, and I expect Marlin as well, I can connect using a generic serial terminal program. On Linux I use Minicom, but any similar program will work if you are using Windoze. When you connect with the terminal program you should be able to send gcode commands just as you did above in Repetier. If things work OK now then it is some issue with Repetier on your system. You might look at other options like bCNC (open source) to interface with your controller. In fact you might want to try bCNC instead of Repetier just to completely rule out something about your configuration is causing Repetier to do something to the configuration of your Marlin settings. Not likely, but worth checking.
7 – If the above steps don’t clearly show where the problem is then my best guess would be that you have something hiccuping with your Arduino HW. Or maybe there is a bug in the version of Marlin that you are flashing with, that is another possibility.
Hope these at least get your started on the troubleshooting path.