Check that you used this key, not an "OrCAD" one:
HKEY_LOCAL_MACHINE\Software\Cadence Design Systems\MasterSettingsFile
16.6 now uses the "cdssetup" like the other Cadence SPB tools, so the CDS_SITE will need to contain cdssetup\OrCAD_Capture\16.6.0 then have the Capture.ini there
Checkout the Capture.ini Manager App on the Capture Marketplace (from the Start Page), this is the recommended way to manage the INI file settings now. AFAIK, the 16.6 version was posted recently.