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Snowy is right, you need to build a case with solid, verifiable evidence. Having a problem with a prof is like having a problem with a cop: you have better be damned sure that when you go above his (or her) head even if they love the cop the evidence leaves them no choice.
I only really had one big problem with a prof when I was in school and I resolved that I would work it out without going above her head regardless of how unreasonable I thought she was being. I waited until I cooled off (please don't go into a meeting heated, ever) and I spoke to a bunch of friends and even a former TA of hers and came in to our meeting prepared. It took some time, but we worked it out and now we're good friends. She even helped me get a job out of school.
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