Yep, you can fix it by changing two lines of code in include/parser.php (in function do_smilies to be more specific):
FIND (Line: 360):
global $smiley_text, $smiley_img;
REPLACE WITH:
global $pun_config, $smiley_text, $smiley_img;
FIND (Line: 366):
$text = preg_replace("#(?<=.\W|\W.|^\W)".preg_quote($smiley_text[$i], '#')."(?=.\W|\W.|\W$)#m", '$1<img src="img/smilies/'.$smiley_img[$i].'" width="15" height="15" alt="'.substr($smiley_img[$i], 0, strrpos($smiley_img[$i], '.')).'" />$2', $text);
REPLACE WITH:
$text = preg_replace("#(?<=.\W|\W.|^\W)".preg_quote($smiley_text[$i], '#')."(?=.\W|\W.|\W$)#m", '$1<img src="'.$pun_config['o_base_url'].'/img/smilies/'.$smiley_img[$i].'" width="15" height="15" alt="'.substr($smiley_img[$i], 0, strrpos($smiley_img[$i], '.')).'" />$2', $text);
Won't have any effect on the smilies on the board itself, other than they use the full URL instead of the relative one.
And yes, it seems to be fixed in SVN.