Strangely enough, the first time I put vinegar in my eye, it stung a little but not too bad, as it did for the second and third time.
I think I've pinpointed the problem.
Kidding aside, I imagine the vinegar is doing pretty much what it does when it preserves food. The combination of salt, acid, and a general lack of oxygen would kill off whatever bacteria is hanging around inside your ear. So, in a sense, you're pickling the inside of your ear.
Hope your ear gets better. My brother went swimming Saturday evening and his ear didn't drain until Sunday afternoon. Now that I think about it, rowdy kids were involved in that case, too. I'm sensing a pattern here...