Our son began doing the same thing around 18mo and has only recently improved at a little over 3. His CF resume reads a lot like your kiddo's (same mutation, MI, pseudo, staph a). My mother, who works in medicine but not w/CF, mentioned that she sees similar behavior in pediatric heart and cancer patients when they come in for routine checkups - and we wondered if he, like them, had simply been though so much at such a young age that he was becoming distrought at the sight of the Dr's office. I'm sure there's also an age factor as others have said.
These things helped for us:
1) priming him for days in advance that we were going to see his 'friend' Dr. so-and-so in a few days,
2) having him tag along to my wife's prenatal appointments (and more recently his brother's well-baby check ups) to allow exposure to a medical enviroment without being poked and prodded - to build up benign familiarity, and
3) following more invasive appointments - getting pizza out and a trip to the store for a big boy toy <img src="i/expressions/face-icon-small-smile.gif" border="0">
It took a while before we saw improvement so be patient - he still freaks with sputum cultures and some probing but has improved a ton from a year ago. Good luck!