--- link.module	2010-07-06 16:54:34.539060510 +0200
+++ link_patched.module	2010-07-06 16:53:26.360616707 +0200
@@ -291,6 +291,11 @@ function _link_load($field, &$items) {
 function _link_process(&$item, $delta = 0, $field, $node) {
   // Trim whitespace from URL.
   $item['url'] = trim($item['url']);
+  // Store system paths
+  $normal_path = drupal_get_normal_path($item['url']);
+  if ($item['url'] != $normal_path) {
+    $item['url'] = $normal_path;
+  }
 
   // if no attributes are set then make sure $item['attributes'] is an empty array - this lets $field['attributes'] override it.
   if (empty($item['attributes'])) {