Quote Originally Posted by DBFIU View Post
Hi Roxy,
The probe only goes up and down once. After it finishes the G28 it retracts, and then extends right before G29. This is unnecessary, how do I stop this from happening?
It is that way because the G28 and G29 should be self contained and do everything they each need. But if you want to change it, you can just call the routine to probe the point in the G28 and tell it not to retract the probe.

Quote Originally Posted by DBFIU View Post
It has to be software related, just has to be...

Is it a version of marlin that is doing this? What about the EEPROM thingy you were talking about? I have no idea how to verify or what to do to confirm if it is that. I need some more detailed guidance, thank you!
You already said up above that the line:

//#define EEPROM_SETTINGS

is commented out. If that is what you are really building, the EEPROM isn't the source of your problem. But the problems you are having sure sound like the kind of thing you would experience if you had a bad value in the EEPROM that was getting used.

Arduino can be very confusing about what project it is loading and compiling. Are you sure you are building the code in the directory you think you are? It might not hurt to go edit a file there so it has a syntax error and then bring up Arduino and verify that the compiler says you have an error where you changed things.