Paulsk,
I believe the QNH you got from your website (999hPa) was no the same X-Plane was working with at that time (1016hPa). Try listening to ATIS (the X-Plane one, not the real one), if one is available for the airfield you are on, it will give you the current pressure X-Plane knows about. Setting it in the Kollman's windows will definitely give you the airfiled's elevation.
Alternatively, set your weather settings to matching real world conditions. And remember there still might be a difference between the real-world data and the sim's one.
Hope that helps.