Hi,
since the beta of version 4 until the current (4.0.3) it simply doesn't remember neither the window position nor the position of the toolwindows. They always start in the corners. I found the keys in the registry where that data is stored, those values simply reset each start.
I have Visual Studio installed, I can send you MemoryDumps, registry exports or you can try TeamViewer to see it happen. A bugfix would be greatly appreciated.
regards
Heyho123