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When averaging starts is the spectrum normal (looking like the RTA plot) or is it already bumped up? If it goes wrong during the averaging something may be getting on to the output, if it is already wrong when the averaging starts there may need to be additional settling time before starting to average.
If you can listen to the test tone while carrying out the test check for any pops or clicks. Also watch out for the interface being assigned as the Windows default for playback, which might allow Windows-generated sounds to get onto the output.
...Try increasing the overlap...