diff --git modules/color/color.module modules/color/color.module
index aa1007c..7761c54 100644
--- modules/color/color.module
+++ modules/color/color.module
@@ -86,6 +86,8 @@ function _color_html_alter(&$vars) {
       foreach ($color_paths as $color_path) {
         // Color module currently requires unique file names to be used,
         // which allows us to compare different file paths.
+        $baselen = strlen(realpath('.').base_path());
+        $color_path = substr(drupal_realpath($color_path),$baselen);
         if (basename($old_path) == basename($color_path)) {
           // Replace the path to the new css file.
           // This keeps the order of the stylesheets intact.