This problem happens at some airports when using Navigraph. The error occurs because the simulator has a data loading order, and with Navigraph sometimes the order is not correct.
Luckily for us, Microsoft came up with a quick fix for this.
Open the simulator, go to options, general options, Experimental.
Activate the Package Reordering Tool option.
A new black window will open
The scenery always has to be on top of the Navigraph, so just locate the scenario you are interested in, and increase the order number, to be above the navigraph-navdata, as in the example below.
Close the window, and restart the simulator using the exit button. Avoid closing the simulator by other means.
Done, now the problem is solved.