Why on earth should this happen cause you're doing dist-upgrade?
And also isn't fastappmanager talking directly to apt-get if I remember right?
I have done this plenty of times when upgrade linux desktops so I dont see why this even should happen in this case, only reason for it to happen is if there is a PR1.3 pending or similar. Or if I do apt-get --purge remove hildon-desktop or similar.