I can sympathise with the cross-contamination nightmare - it's why I rarely eat out. I've got no idea whether there is a scientific mechanism for it, or even if it's physiological at all and not just mind over matter, but I've noticed that I seem to react more to stuff if I've been a bit under the weather for a few months. Or put the other way round, I've noticed I'm so much generally healthier in completely daft and unrelated ways now I'm doing loads of exercise. Wierd, huh?
I get the same effect - if I'm generally under the weather my IBS is much more easily set off. Wouldn't know about the effects of a lot of exercise though, since I'm allergic to that as well ;-)