Wayne,
This seems like a rather strange position for me to be in, (about to try to defend a GI doc -

), but some of what he said, has merit. I'm going to stick my neck way out, (because I haven't researched this at all), and point out that environmental test labs are very likely held to a much higher standard, than medical test labs. Even though that sounds crazy, (and it might very well be crazy, for all I know), here's why I think it is so: Environmental test labs are governed by law, and the laws are very strict, concerning most issues involved. (According to the law, if you accidentally step on an endangered salamander, and squash it, being blind, is not a defense). IOW, much of the law that apples to environmental issues, does not allow for exceptions, and violations of those laws, can result in huge penalties, because the government is involved, and the government is not inclined to be forgiving - the law is the law.
Medical labs, on the other hand, operate under a much more flexible set of "rules and regulations", set up by medical authorities, not the government. I would venture a guess that the medical industry is pretty much "self-policing", for the most part. I suspect that mistakes made in a medical lab, are viewed not much differently than mistakes in the operating room, a doctors office, or a nurse's station. They are regrettable, of course, but mistakes happen, so a lab mistake is not the "end of the world", from a judgmental perspective. It is left up to the doctor to be the judge of whether or not a lab result should be trusted - that's part of his or her job.
I may be all wet on this theory, but Polly can probably shed some very illuminating light on the issue. The bottom line is, IMO, mistakes are not exactly a rare item, in medical labs. Most mistakes are probably due to paperwork errors, sample mixups, etc., but they probably happen much more often than we would like to think they do, and I doubt that someone's head rolls, on most occasions, when a mistake is made.
I believe that he's right to check for possible muscle damage, also, to narrow down the possibilities.
His plan, "to see it the microscopic colitis has resolved ...", is worth a good laugh, I suppose, but trust me, that ain't gonna happen. Even if you were to do everything exactly right, the histology of your intestinal epithelial cells, probably would not be resolved in two years. GI docs don't have the foggiest idea how long it takes to heal the damage caused by MC, and/or gluten, if you are gluten sensitive.
I have to agree with him on the breath tests, also. Research has shown that those tests rely far too heavily on the subjective judgment of the operator, and most operators are simply not skilled enough to consistently make sufficiently accurate judgments on test results. Unless the operator is exceptionally skilled, you might as well flip a coin. I can track down research references to verify this conclusion, if you need proof, but I don't have time to look it up right now.
Wayne wrote:He called me his "problem child" I guess because I do not seem to be making any progress.
Here is where he totally loses my support. Whenever a GI doc becomes frustrated with his own shortcomings, and begins to be annoyed, because a patient is not making any progress, despite trying all sorts of things, an insecure GI doc will try to assauge his or her ego, by transferring the blame to the patient. Of course, in this case, he may have been jokingly referring to you as his "problem child", since he didn't come right out and say that you are the only patient who has ever failed to respond to his treatments. Usually, they will also throw that at the patient, in order to be sure that the patient clearly understands that it couldn't be their, (the doctor's), treatment that is at fault.
All in all, at least he seems to be trying. Hopefully, he will be able to track down and resolve those enzyme issues. He seems to be comfortable dealing with that, at least.
Tex