I'm feeling pretty embarrassed.. When doing an initial adjustment I was tying to go for a "knee-over-pedal-spindle"! But instead I was trying to make my knee do 90º with the ankle!
I'm still a student, in the future I intend to have a bike professionally fit. Right now I simply can't afford that, and in my ignorance a bike two sizes smaller didn't seem to be a problem. And it seems.. it isn't! knee over ankle.... *sigh*

The stem is 100mm. I'm not very flat, but for now that's ok. The saddle is a San Marco Rolls, btw.

Thank you very much cyclezen and 36Oly_Rider! I will follow your advice.