I wonder if anybody else noticed change in AIR 2.5.0 wich is connected to mouseX/mouseY property on DisplayObject. In older versions (AIR 2.0.4 and older) mousex/mouseY returned different values after clicking on e.g. Image object then in newer AIR versions.
As the prove that something changed you could try Adobe example from their live documentation : User Interfaces / Using Drag and Drop / Drag and drop examples. Try the first example (which works with mouseX/mouseY property) and run it as AIR application (with WindowedAplpication tag - with Application tag it works just fine). It didn't work with my old AIR 1.5.1 but it did work with AIR 2.5.0.