In general there's a difference between signal strength as returned by the NMEA data (also known as AMUs - Arbitrary Mystery Units, see http://gauss.gge.unb.ca/papers.pdf/SNR.memo.pdf) and the signal quality.

I don't know whether you are working out the quality of the signal with your signal analyser (e.g. by processing the data using something like this: http://www.l3nav.com/gps_toolbox.htm)?