I'm recently doing a lot with GlissEQ (which is meant as a compliment! :), including some rather "technical" stuff (sorry, I have a strongly technical background).  Recently, I pushed white noise through GlissEQ, and while that displays correctly as a flat line when "Slope" is set to 0.0, it seems that when I apply EQ (no matter if I use GlissEQ itself or a different EQ), the spectrum display is off by a factor of 2.  For example, if I apply a peaking filter at 1 kHz with 18 dB gain, the graph will only show 9 dB:

http://pub.instinctive.de/glisseq.jpg

A different spectrum analyser correctly shows an 18 dB peak.

Well, "factor of 2" is of course wrong -- the dB scale on the left is off by a factor of 2, actually.

You are right - spectrum does not follow dB scale on the left.  dB scale on the left is for the equalizer.  Spectrum display is meant to be adjusted visually - there is little need for exact dB values.