Sean talks more at http://blogs.msdn.com/vseditor/archive/2005/05/12/417011.aspx

Quick summary:

  • To avoid issue – try not to set tool windows to auto-hide.
  • Experiencing issue? – activate the auto-hiding tool window and close it

I personally haven’t hit this issue, but others have.  I guess I can’t have all the bad luck in the world – just a lot of it =)