Thank you for your advice - it makes a lot of sense. The only thing that boggles my mind is that they hired me because I'm an expert and I'm good at what I do - yet when I take initiative, the boss freaks out.

Have you ever lived somewhere where the new roomate decides to streamline the way the kitchen operates, and you can't find anything for six months?

I just want to suggest that what's going on here may not be entirely a technical issue, but a social one. Your boss may be using CVS history as an excuse, when really it's his own mental flexibility that's a problem: if every new guy that walks in the door rearranges everything -- and every new guy wants to, that's a given -- then he's never going to know where anything is.