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Only way it could happen if you randomly open existing workbook with 9.3 and save it there.
Right-click on any workbook, pick "Open With" then "Choose default program" then choose "C:\Program Files\Tableau\Tableau 9.1\bin\tableau.exe".
This should set default association of Tableau workbooks with 9.1. You'd need to do that for all Tableau files you deal with (twb, twbx, tds, tdsx, tde).
That is exactly the issue! I didn't open from within 9.1 so it defaulted to 9.3.
Please note that installing new versions of Tableau will override associations so double-check that once in a while.
Not sure if upgrading (i.e. maintenance release) will do that or not though...