Excerpt: h3.../h3 becomes p..., but no closing /p
 

The post's fragmentin an excerpt becomes:Note the absence of closing "/p". I am not even sure if this is Atahualpa's issue or Wordpress issue?

URL?
Is this a manual excerpt or atahualpa excerpt?

goo.gl/CKiLg and search for "When to call?". I think it's an automatic excerpt.

If you want the text to have the <h3> surrounding it, then go to ato->Configure excerpts and add <h3> to the things not to strip

Oh no. It would have been perfectly ok to have the <h3>...</h3> converted into <p>...</p>. What is not ok is the </p> missing!

What version are you on?

WP 3.3.1, Atahualpa 3.73.

I was able to reproduce the issue in a sandbox (local PC) even with all plugins deactivated.

Yeah, I reproduced it. It something that crept into the code due to a change between 3.4.9 and 3.5.1 - I've tracked it down a bit and have forwarded my findings to the developer and am waiting on a reply from him.

Interestingly, it only happens to the <Hn>...</Hn> and doesn't effect other HTML codes like center or strong

Wow! glad you tracked it down. I noticed the issue accidentally, by running validator.w3.org, and this was such a minor issue I doubted whether to post it to the forum at all.