the phase noise plotted is dBc/Hz (decibel from carrier per Hertz) so is in reference to some carrier level.
when the reference harmonic is 1 (lets say this the oscillator frequency= 1GHz), then you get the phase noise in dBc/Hz with reference to the fundamental "carrier" signal level at 1GHz.
when you do the phase noise with reference to harmonic 2, indeed your dBc/Hz phase noise plot may look like its bigger, but this is because you are now referencing a carrier level at 2GHz (which in your case is probably very small compared to the fundamental carrier at 1GHz). You can check the difference in the levels between the carrier references at 1GHz (harmonic 1) or 2GHz (harminic 2), by looking at your pss results.
see this related topic below to help further your understanding, where here now the refernce harmonic for the phase noise plot is fixed, but the sweep pnoise sweep goes past the 2nd harmonic:
http://www.designers-guide.org/Forum/YaBB.pl?num=1174556880cheers
aw