Cool, the update problem only occurrs with some updates, service packs in particular, basically ones that involve that system file, it sees it's not standard & stops, just in case it's not standard for good reasons... it will happen regardless if done manually or with tune-up, although tune up may set it back, but why mess with it in any case? it's not like win 98 where systems crashed constantly & you saw it every few hours.. it's often weeks between me seeing my boot screen....
messing with system files routinely is a bad idea.. the modification only has to go wrong once, & in this case your system would be rendered unbootable