I reinstalled Python (noticed I could run the program, but it wasn't listed separately in the Add/Remove programs page) and then ran the microsoft registry fix tool, following the prompts and indicating that I wanted to uninstall ArcMap 10.3.1. This worked and I was able to install 10.4.1 after that. I had tried renaming (_old) the ESRI keys in the registry and removing all ESRI folders, plus changing the location of My Documents back to my computer rather than a network share. None of that worked.
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We are having this exact same problem with Shapefiles exported from VISUM. Everything looks fine in 10.1, QGIS, even Excel, as well as Pro, just not in 10.3.1. I agree, this is a major issue and should be addressed before 10.4.
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