i bought a FSA SLK last summer for my bike.
at first it was very uncomfortable. i spent a while fiddling with saddle height, fore-aft positioning, and stem/bar combination. basically, saddle comfort is part saddle, and part your entire fit on the bike.
anyway, one day it just sort of up and clicked into a certain level of comfort. huzzah, eh?
also, some undies/pants are more comfortable for me than others, just due to the way they hold my jams while i'm pedaling, which refers back to how easily i position myself for comfort...