<<To be honest, I don't have much faith in doctors at all really. >>
Join the club, honey! I think you'll find a lot--probably most--of us here don't like doctors all that well either. We've all been put through the mill with tests that come back negative only to have doctors shrug and hurry us out the door. Even if there's not a whole lot you can do for IBS, they could at least be sympathetic!
I don't really understand what your nutritionist told you. It sounds like she's telling you you have holes in your stomach and stuff is leaking out. If that was happening, you'd certainly know about it!!! Namely because you would be septic (i.e. have an infection). When food is digested, it's broken down into useable pieces and is absorbed through the stomach and intestines and is carried through the body to the cells that need those nutrients to survive. I don't think that yeast is getting into your bloodstream any differently than any other food that you consume. This is quite apart from being allergic to it. You may certainly be allergic to wheat or other foods; some people with IBS are. And your allergic reaction to these foods, along with the fact that bacteria can cause ulcers can contribute to an erosion of your stomach lining, esophagus or intestines. But I don't think that an ulcer is the same thing as having a hole in your stomach. Nor do I think that certain foods are "escaping" through your skin. Again, this is quite apart from exhibiting an allergic reaction. I think basically what she recommended for you is probably correct, but she explained what was causing your problems it in a really bizarre way that doesn't make any sense.
If you didn't take the test through a clinic or doctor (if was something you bought online and mailed off yourself), then I would suggest you go to a doctor or allergist and ask that they test you for food allergies. That way you can be certain that you really are (or are not) allergic to certain foods and your doctor can help you find a nutritionist that can help you eat. There is also the fact that there's a difference between an intolerance and an allergy. And even "intolerance" has a range from mild to severe. A good test should tell you how intolerant you are. And your doctor or a nutritionist should be able to say, "Well, since you are mildly allergic to that, I wouldn't recommend you eat more than x grams of it a day," or "you can eat it when it's a small part of a complex recipe, but don't eat anything where it's the main ingredient."
It's not enough to say, "Oh, don't eat bread or anything with wheat in it;" you have to know all the different technical names for wheat and its by-products. A registered nutritionist should be able to give you a list of all the words to look out for on food labels and even a list of commonly-purchased foods that contain hidden wheat ingredients (just about everything, actually). Even milk proteins pop up in foods that don't look like they would contain milk.
In the meantime, I definitely recommend the calcium. It helped me. Also, don't stop the probitoics if they are not causing you any problems (acidophillus by itself gives me gas cramps, but it's okay when combined with other stuff in yogurt); probiotics are always good for you and if you do indeed have a bacteria or yeast overgorwth, they will help, although it can take some time to see a difference.