There have been so many reports of floating buildings at Skagway that there has to be a problem of some kind.
On the ORBX forums the 'official explanation' is that "this is a known FSX anomaly and there is nothing that can be done about it". What seems strange to me is that if this were true, in my opinion, it would be rather common for everybody in more than just Skagway.
While FSX 'problems' may be partly at fault I simply do not buy it that floating buildings are common at only one airport. I think there is more at work and common sense tells me the ORBX scenery used at Skagway must have something in it allowing the FSX problem to manifest itself more than other locations.
As far as opening the Scenery Library and clicking OK to rebuild the scenery database to correct the floating buildings will work it will also cause all the AI shipping to double up and you will see two ship following one another along the AI tracks which is not an option that I think is viable.