I have tested Rebellion retail and the shadow bug is still there, as prominent as ever. I believe the shadow bug has two major contributors to it.
The first contributor is that the shadow maps are extremely small. The 'squares' we're seeing are no doubt individual pixels of the shadow map. I thought maybe you could force higher resolution shadow maps in the settings file (Why waste all my GPU power, anyways?), but such is not possible.
The second contributor is that the engine doesn't seem to devote nearly enough shadow space to edges or thin constructs. This makes sense to an extent, but every single attennae in the game seems to create wildly flickering shadows, not to speak of curved wings, plating, and other such things. Some shadows create triangles and not even "pixels", resulting in very weird shadowing.
The attennae on the new TEC capital ship also produce very buggy shadows.
I seriously doubt a new version of convertxsi.exe would fix this, unless it allows you to manually define the resolution of a mesh's shadow maps. A lot of ships like my Kraken above have a lot of plating and tests yielded it all freaking out because of these bugs, and the bugs are prominent on many vanilla meshes.
Changes to AF and AA settings have no impact on the bug. While I zoomed in to point out the bugs, you'll see them clearly at any distance, especially if the ship is moving.