Welcome to the IBS board!
IBS can indeed be stress related. It is not too uncommon for anyone to have bowel trouble when they are super stressed out. I have friends that complain about
this phenomenon a lot... I tell them "Sucks, huh? Try having that D all the time." It could be that you just have a nervous stomach. And yes, it could also be an autoimmune disease that is causing you these problems. It could even be a combination of both.
I don't know about
autoimmune disease, but IBS cannot interfere with any of your HIV tests. Unless you are on any medication, IBS does not hinder or err anything but your convenience.
We do have at least a couple members on this board with autoimmune diseases... Maybe they'll have some input for you.
All I can suggest at this point is to try some stress relief.