Hey Vladimir,
Artem here from AndroidPolice/BeerPlanet. I've been using your excellent plugin to auto-link for a while and since I'm using Windows Live Writer, I've been seeing this problem that I finally decided to report.
Basically, your plugin is not supposed to overwrite links that already have existing hrefs, but it seems to do it if there's a tag inside the <a> tag. For example, if you italicize a sentence in WLW, it adds <em> tags inside each <a> tag, like so:
<a href=foo><em>SEOedText</em></a>
What should happen is SEOedText is supposed to retain a link to foo, but it doesn't and instead points to bar, which is what is set up in the plugin's replace list.
Thank you.