A while ago I published what I thought was a fix for fixing the Visual Studio 2008 bug that occurs when stopping debug after having moved the Solution Explorer, Output windows debug windows. Visual Studio 2008 closes at build, Outlook 2007 Add-In
After having just re-installed my machine I attempted to fix this same problem with my documented fix, but alas it did not work. It turns out that the Visual Studio Shell Team has released a Hotfix for this issue, and it works!
Details on this fix can be found here on Code.MSDN or Microsoft support.
Hope it helps.