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Oh, with your answer I think I found the issue. I'm using windows mklink /j command to keep all my code in one location and use the code elsewhere on my system. When I'm debugging the file pops opens from the alternative location, because the full path to the files differs from the project path.

e.g: /github/code_folder/myscript.py

links code_folder to :

/documents/maya/scripts/code_folder/myscript.py

The debugger opens the maya path. That's probably not a bug vs. an issue with my setup. Dang.