The first one is the link to the home page of your wiki, the second one a link to the main page of the subpage. They are the same only on sub pages of the home page. If you are confused by this behaviour you could do the following change in the source code:
in sub GetGotoBar:
$bartext .= " | " . &GetPageLink($main);to
$bartext .= " | " . &GetPageLink($main) unless ($HomePage eq $main);
There may be other oddities with regard to subpages.