Upgrading would indeed wipe out your changes.
I'm personally running 1.6ST and have clickable urls enabled, and have not experienced the problem that you are describing.
There is a clickableURLS function in 1.6st is located in \include\class.config.php. You may want to compare it to your version. Line 245 is the start of the function.
There is also in \include\class.format.php circa line 84 a reference to it. You might want to compare that to your version also.
function display($text) {
global $cfg;
$text=Format:($text); //take care of html special chars
if($cfg && $cfg->clickableURLS() && $text)
$text=Format:($text);
and again on line 97.
//make urls clickable. Mainly for display
function clickableurls($text) {
//Not perfect but it works - please help improve it.
$text=preg_replace('/(((f|ht){1}tp(s?):\/\/)+)/','<a href="\\1" target="_blank">\\1</a>', $text);
$text=preg_replace("/(^|)(www\.(+(\.+)+)(\*)*)/",
'\\1<a href="http://\\2" target="_blank">\\2</a>', $text);
$text=preg_replace("/(^|)(+@(+\.)+{2,4})/",'\\1<a href="mailto:\\2" target="_blank">\\2</a>', $text);
return $text;
}
I didn't really see anywhere else in the source that references it but I also looked very quickly.