After looking into this further, I think the issue may be with one of the functions of Get Recent Comments itself, rather than any differences between get_permalink() and the_permalink(). Although the links generated by the plugin were missing the URI specified above, the code that was generated in the sample that’s seen on the Options -> Recent Comments page had properly formatted URLs. To get around this, I simply swapped out the function that creates the actual recent comments code on the site with the function that creates the sample. This :
function get_recent_comments()
{
echo kjgrc_cache(“comments”);
}
…becomes this :
function get_recent_comments()
{
echo kjgrc_create_recent_comments(“comments”);
}
I’m not all that familiar with the detailed differences between these two functions that would make one work and one not, so if anyone else has this problem and decides to employ this workaround, I’d suggest closely monitoring your site for any potential problems.