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I suspect you have pep 8 reformatting enabled in the Editor > PEP 8 preference area. It looks like it might be running a pep8 format, although I'd expect spaces before all the comments (but then autopep8 can be a bit weird).

If that is the case it may be that unchecking the Editor > PEP 8 > Spaces After # preference will solve it.

If that's not it, please let me know.