I've been struggling with this issue too.
Every time I open VS2008 then my output window, task list, error window are all full size and not docked at the bottom.
I've saved my .vssettings file to a new location which I have given All rights to. This did not solve the problem with my windows size and placement.
Probably due to what someone said about that data being saved in the .prf files at:
%APPDATA%\Application Data\Microsoft\VisualStudio\9.0\windows.prf
I only want the default behavior for those windows -- docked at the bottom.
So, then under the VStudio 2008 Windows-->> menu item, I find:
Reset Window Layout
I click that and the windows are all set properly.
However, after I close and re-open VStudio 2008 then all my other preferences are saved:
External Tool Items, Custom toolbars, custom buttons on toolbars
But, the window locations are not ever correct. I am resolved to clicking the :
Reset Window Layout
But, this is a really annoying bug in VSTudio 2008.