Yep I had the same problem! I said the same thing as George P., isn't that the point of an inspection? I am pulling a permit and scheduling an inspection to make sure I do the work correctly! You run into shady jobs when there are no permits pulled! But people trying to do it correctly get screwed.
My problem was plumbing. I bought a foreclosure that needed a complete plumbing rehab, from the water lines in to the vent/waste pipes leaving. Tore out the whole kitchen and bathroom. I ran all the plumbing with the help of a licensed plumber (but not licensed in the city of minneapolis, which is needed in minneapolis). Pulled a permit and had the inspector come out, he was in the house for no more than 5 seconds and walked out saying he can't inspect it.
I called the building department office and came to the conclusion that I can't do any plumbing work on the house unless I live in it, and by law I can't live in a house that doesn't have a working toilet. I had to hire a licensed plumber to go to the city and pull a permit. He charged me $500 in addition to the cost of the permit (which I already pulled and paid for once).
I am putting in another bathroom and do not want to pull another plumbing permit, but I know it will bite me in the arse if I don't. I don't understand why people trying to do the right thing get crapped on!