Pages that use PHP and rel="lightbox" tags get into trouble when TinyTinyMCE is enabled. Rather than trying to solve each of these issues independently, why not just provide a way to prevent TinyTinyMCE from loading altogether on pages where this kind of code is needed? (i.e., the same "load on every page / load just on this page / load on every page but this" functionality we have for Drupal blocks.)