[Plugin: Broken Link Checker] Valid anchors found broken with subdirectory-installed WordPress

I have my WordPress installed to a subdirectory, and use htaccess to bypass/hide it.

For most posts, this plugin works fine. However, in one, I have simple anchors that are coming up as broken.

The links look like this:
<a href="#anchor">anchor</a>

Broken Link Checker thinks these are broken and in the “Broken Links” list, their URLs are being incorrectly displayed as:
http://domain.com/SUBDIR/post-name/#anchor

… when they should be displayed as:
http://domain.com/post-name/#anchor