I'm seeing the same problem. This happened early in the beta, but seems to be back. I have a dual-monitor setup and consistently see the problem. I have VA view on the first monitor and the classview/output/task windows on the second monitor. When I first start VS it starts minimized. If I try to click on the icon in the taskbar VS doesn't respond. I have to right click on it and click "Restore" and then "Maximize" to get VS to open. Once I have VS open the VA View (and any other windows docked with it) is not docked correctly. It's painted, but it looks like VS doesn't recognize it. My file tabs extend all the way to the side of the monitor, but VA view is painted over top of them. After this happens I have to go to Reset Windows Layout for the window to respond correctly.
I have this with VS.NET 2002. I haven't seen it on 2003. (My computer with 2003 does not have two monitors though)
I also have a second monitor. The black window is on the first monitor on the right side.
For now I "workaround": I compile and run my program. After this the windows on the first monitor are rebuild and now the VA View is on the right side on the first monitor. Now I can move it to the second monitor.