Hey I went through my file again and noticed one difference...
I revised my code on line 114 to as follows and it works perfect now. (Bold is inserted, not coming through correctly should include brackets).
$link = sprintf('<a href="%s%s" title="%s"target="_blank">%s
</a>',$link,htmlentities(urlencode(trim("$volume $book $verse"))),$title,trim($reference));
BTW, great hack, thanks a lot!
Verlin