Hi @dezzdot,
First, my apologies for the lateness of my reply, it’s been…well, a year!
Advanced Post Excerpt does not change the way that excerpts are rendered within WordPress, but rather presents a TinyMCE editor to editors to help them construct excerpts (as opposed to manually writing HTML). Are you able to confirm that the HTML is making it into the wp_posts.post_excerpt column in the database?
If the HTML is being stripped out on the front-end of your site, your theme is the likely culprit. It’s not uncommon for some theme authors to get a little aggressive when escaping output, and may hook something like PHP’s strip_tags() function into WordPress content-related filters (such as “the_excerpt”).
Another possibility would be the types of HTML elements being used; by default, WordPress will run post fields through wp_kses_post(), which uses a (filterable) subset of allowed elements and attributes.
