OK, so it wants a trailing slash...

functions/auth.php

@@ -16,7 +16,7 @@
  */
 
 if (!isset($base_uri)) {
-    $base_uri = dirname(dirname($PHP_SELF));
+    $base_uri = dirname(dirname($PHP_SELF)) . "/";
 }
 
 function is_logged_in() {

src/login.php

@@ -69,7 +69,7 @@ set_up_language($squirrelmail_language, TRUE);
 /**
  * Find out the base URI to set cookies.
  */
-$base_uri = dirname(dirname($PHP_SELF));
+$base_uri = dirname(dirname($PHP_SELF)) . "/";
 @session_destroy();
 
 /*

src/redirect.php

@@ -36,7 +36,7 @@ if (get_magic_quotes_gpc()) {
 
 /* Before starting the session, the base URI must be known. Assuming */
 /* that this file is in the src/ subdirectory (or something).        */
-$base_uri = dirname(dirname($PHP_SELF));
+$base_uri = dirname(dirname($PHP_SELF)) . "/";
 
 header('Pragma: no-cache');
 $location = get_location();

src/signout.php

@@ -35,7 +35,7 @@ if (!isset($frame_top)) {
 /* If a user hits reload on the last page, $base_uri isn't set
  * because it was deleted with the session. */
 if (!isset($base_uri)) {
-    $base_uri = dirname(dirname($PHP_SELF));
+    $base_uri = dirname(dirname($PHP_SELF)) . "/";
 }
 
 do_hook('logout');

src/webmail.php

@@ -21,7 +21,7 @@ require_once('../functions/plugin.php');
 require_once('../functions/i18n.php');
 require_once('../functions/auth.php');
 
-$base_uri = dirname(dirname($PHP_SELF));
+$base_uri = dirname(dirname($PHP_SELF)) . "/";
 
 session_start();
 is_logged_in();