site in subdirectory does not get correct base_path() for links

site is in subdirectory at http://www.domain.com/knowledge/

but had to change line 205 or taggly.module function theme_taggly_contents()

$base=base_path();
to
$base=base_path()."/knowledge/";

for correct links

I checked pathauto aliases and base URL in settings.php, but this is the only way to make it work