Just as an FYI,
All of the volume levels for both audio out and record in should be at the max and the balance be set to the middle. If your settings are not these you will possibly see anomalies (i.e. strange spikes or dips, jagged plots, etc...) in the plot graphs.
Also in Vista on some systems the USB ports can be individually adjusted, so if you set it up on one port for testing and then the next day use a different port you may see anomalies in the measurements.
And as stated in the article there is a 90 second stabilization time for the unit, it is necessary to wait otherwise there will be anomalies in the test graphs.
And if you have it set up properly and calibrated and are getting strange graphs there could be two other causes:
1) Other noise in the testing area (i.e. kids, dogs barking, etc...) these things will affect the plot (testing should be done in a semi-quite room.
2) The .ini file became corrupted, just delete it and restart the WT3
Hope this helps.