This is just a guess on my part regarding vinegar.
I did an extensive cleanse (about a year long) for candida a while back. I learned that vinegar is very high in yeast. Perhaps you are reacting to yeast rather than vinegar per se.
During a strict candida diet, no fruit is allowed especially for the first three months due to the high degree in Sugar and (with some fruit) yeast. After that, just the occaisional low glycemic fruit (eg: apples.)Certainly no citrus!
Maybe you can test the yeast theory by trying something else with high yeast content (grapes?)
I now only use apple cider vinegar - it is recommended by many health practitioners including Burroughs in The Master Cleanser .