I saw this exact same thing back in DG IV beta testing, but it was a graphics client issue only, and it was fixed.
But first off, well welcome back to orbiter. One of the things that have changed since you were away is that there are now 'Graphics clients', which are made by some very dedicated orbinauts. There are a few of then, but by far the most popular, most complete and most stable is the Direct X 9 graphics client, which most people will just refer to as the D3D9 client.
I highly recommend looking into using it. In my opinion it should be considered the standard Orbiter environment now because it offers so many benefits over the vanilla in line Direct X 7 client.