Two points really - where is the water vapour coming from and why is it not getting out!
1) Did you put a DPM down under the concrete to prevent moisture in the ground getting through the concrete? If not , that's where the source of the moisture is coming from.
2) Once in, it can't get out. Flat roofs aren't particularly permeable to water vapour either, but polycarbonate certainly aren't. Could you allow for a vent to be constructed where the polycarbonate crosses over the top of the UPVC window frame, to allow air in? If not, a ridge vent, perhaps?