Dudly,
I sometimes get a black square in my 2d cockpits. I'm pretty sure it's a gauge that causes it. Seems my little black square showed up when I first installed Saqson's (Kochmarsky's) neat little F2F Buffalo. Every now and then I see it in another plane too, but I just right click on it and select "Close Window" and it goes away.
Now days with Thicko's Buffalos, I haven't seen it much.
I don't recall seeing it in the VC. Which plane do you see it in?