I have been having this issue with ArchiCAD 11. It is frustrating that this problem still exist in the newer versions of ArchiCAD.
Like you, I have experienced this on both AC windows and third party windows.
Other observations: Changing the angles of the shadows help, but not entirely... for example, if I changed shadow azimuth, shadow casting on some of the windows would be corrected, but other windows would still show incorrectly.... the crazy part is, the windows are placed on the same wall and are completely identical but still, one would show shadows correctly and the other would not. There is no consistency with this issue other than, its a bug.
If there are others with this issue or someone with a fix, please chime in.