I have the same problem as the gent who posted this:
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. :)