I don't believe it is adding it every time, as I have done lots of manual program updates (to test this, on my XP Pro system) and for me it never once asked for a reboot as the manual update said there was no update present and I clicked OK. So I never got asked to reboot.
The only reason I can think of is an out of sync situation where the current and reported program version are seen as different. In the same way as the manual VPS update check says you are up to date, yet the displayed version is different. So I don't know if the repair function would resolve the out of sync situation as it has in the past.
For me, the question is still, why it is the registry key still there after a reboot, is it ?
If so, it is likely to be some form of registry protection on the effected systems.