I have the same problem as the gent who posted this:
http://wordpress.org/support/topic/plugin-broken-link-checker-custom-fields-cause-phantom-broken-links
In short, we're not really able to make it check custom fields created by the Advanced Custom Fields plugin. ACF seems fairly prolific; any chance we could get some built-in support for it? I don't know about everyone else, but I personally would be delighted with just a checkbox on the What To Check tab for 'Advanced Custom Fields'.
Love the link checker, SO want it to work on all the content. :)
Thanks!