I've found that on your file com_akeeba/models/cpanels.php you are comparing file permisions of media/com_akeeba with 40755 without the leading 0.
I've added the leading 0 as you can see next and the "media/com_akeeba" error message disappeared.
line 180: if (($parentPerms != 0755) && ($parentPerms != 040755))
line 207: if (($perms != 0755) && ($perms != 040755))