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Never ever ever ever ever ever install Windows over top of an existing installation; I don't know if that's what you meant by re-installing programs or not. Never do -- it'll make the situation worse.
If you plan to re-install windows, get everything important backed up off the drive, format the drive, and insert the windows CD. The rest is straight forward if you've done it before.
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"I'm typing on a computer of science, which is being sent by science wires to a little science server where you can access it. I'm not typing on a computer of philosophy or religion or whatever other thing you think can be used to understand the universe because they're a poor substitute in the role of understanding the universe which exists independent from ourselves." - Willravel
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