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.
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.
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