I use main autoloader with enabled warnings and fallback autoloader. I also use modules bootstrap with Zend_Application_Resource_Modules.
When I try to define routes for my module via module prefix as it's desribed in the manual e.g.

blog.resources.router.routes.blogIndex.route = blog
blog.resources.router.routes.blogIndex.defaults.module = blog
blog.resources.router.routes.blogIndex.defaults.controller = index
blog.resources.router.routes.blogIndex.defaults.action = index
blog.resources.router.routes.blogIndex.type = Zend_Controller_Router_Route_Static

I get these warnings

Warning: include(router.php) [function.include]: failed to open stream: No such file or directory in blabla/zendframework/library/Zend/Loader.php on line 83

Warning: include() [function.include]: Failed opening 'router.php' for inclusion (include_path='blalba;....') in blabla/zendframework/library/Zend/Loader.php on line 83

Maybe cause is same as in ZF-6658

if (class_exists($plugin))

in Zend_Application_Bootstrap_BootstrapAbstract::getPluginResource()