I also don't use fuzzmeasure, so I don't have anything to add on the software setup.
However, are you sure there is no low freq AGC (auto gain control, compressor?) somewhere in the input chain? What mic, pre-amp/soundcard set up are you using?
The only other thing I can think of is some low level external noise that may have been picked up ie other than the test sweep. Have you tried the same set up in another room? If you get the same LF late onset increase in level then there is probably something wrong with your set up?