Very odd. I put:
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into every occurrence of Base File.sublime-settings I could find (default, user, and the one in sublimelinter). Figured this would help me determine which Base File it was expecting to find it in. I put a "print map" statement in the module_utils.py to see what was happening and to make sure it wasn't just me putting in an invalid path, and, unfortunately, it consistently shows "None".
My original thought was it was something screwy about using "Base File" in the sublimelinter folder, since changing the name of the file from "Base File.sublime-settings" to "SublimeLinter.sublime-settings", and then adjusting the module_utils.py file to reflect the same resolved the issue. But with you being able to get work makes things just that much more confusing. Thanks for checking.