I haven't seen Windows Genuine Advantage (WGA) be a problem on any of the hundreds of machines I have ran the windows repair on.
Are you using a cracked version of Windows? If your using remove WGA I take it you are.
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I have no clue on the process to remove wga and how any of the repairs have anything to even do it that would trigger it to show up. No a single repair touches anything with WGA.
Microsoft does put out updates that look for WGA being removed so keep that in mind.
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Microsoft has also been known to push silent updates out without the user knowing.
But I wont help to crack Windows WGA. Thats just asking for trouble. Sorry bud.
Shane