For me, I reckon it's because my ears have become sensitized to anything that sounds a bit out of tune, or maybe, my ears have learnt how to recognize when an instrument is out of tune, my theory anyway, I think that once your ears learn how to recognize out of tune-ness, it's very hard for them to un-learn it, for some people, it tends to drive them up the wall so to speak, other people seem to be able to tolerate some out of tune-ness.
Anyway, I'll keep posting updates on this project, I might give the Hot Rod Strat a few more coats of paint tomorrow and then let it dry for a couple of weeks, then I might do some clear-coating.