Heating mystery following replacement windows
OK Let me try. Originally you had your single zone heat on. My experience is first floors are usually warmer than second floors. Hot air wants to rise but it can't unless there's some cooler air replacing it. That's where the drafts come in from the older windows on the first and second floor. So heat rises to the second floor in addition to the second floor heating and all is well.

Then you change the windows. No more drafts from outside. Now the hot air on the first floor can't rise like before because there's no air coming in because no drafts. The second floor now has to rely on only the second floor heating which is usually lower then the first floor heating, single zone.

End result, a warmer first floor and a cooler second floor. Try to regulate the first floor heating, close the valves a bit so hotter water get to the radiators on the second floor. Good luck