Я помню у меня MSDN не ставился повторно и не деинсталировался.Может здесь такая-же ситуация ? Вот что написано по поводу "правильной" деинсталяции MSDN перед повторной инсталяцией :
Uninstalling this release
To remove MSDN Library from your machine, run Add/Remove Programs from the Control Panel, select Microsoft Developer Network Visual Studio 6.0, and click Add/Remove. After this program removes Microsoft Developer Network Visual Studio 6.0, check the Microsoft Visual Studio directory to make sure all of the MSDN98 files have been removed. If not, delete the MSDN98 directories manually. In addition, the following manual removal steps are recommended:

Uninstall MSDN Library - Visual Studio 6.0. Select Start, Settings, Control Panel Add/Drop Programs. Click on Microsoft Developer Network Library - Visual Studio 6.0 and click the button Add/Remove.
Delete HHCOLREG.DAT and HH.DAT files in the Windows directory.
Delete the HHCTRL.OCX file in the Windows\System directory.
Delete the HHCOLREG.DAT file in the Windows\Help directory.
Then use the Registry Editor (regedit) to remove the desired collection key(s):

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\HTML Help Collections\Developer Collections