I've symlinked my plugins directory and had a problem with the path defined for SCOPER_ABSPATH. The following is a patch that works for me and should be flexible enough to work with any system.

Index: role-scoper/role-scoper.php
===================================================================
— role-scoper/role-scoper.php (revision 16362)
+++ role-scoper/role-scoper.php (working copy)
@@ -135,7 +135,7 @@
 if ( ! defined('WP_CONTENT_DIR') )
        define( 'WP_CONTENT_DIR', str_replace('\\', '/', ABSPATH) . 'wp-content' );
 
-define ('SCOPER_ABSPATH', WP_CONTENT_DIR . '/plugins/' . SCOPER_FOLDER);
+define ('SCOPER_ABSPATH', WP_PLUGINS_DIR.DIRECTORY_SEPARATOR.basename(SCOPER_FOLDER));
 
 define ('ANON_ROLEHANDLE_RS', 'wp_public_reader');
 
@@ -237,4 +237,4 @@
        add_action('set_current_user', 'scoper_maybe_init', 2);
        add_action('init', 'scoper_log_init_action', 1);
 }
-?>
\ No newline at end of file
+?>

I'm going to use WP_PLUGIN_DIR instead, which is defined by default.