Guys I have the following structure in my project.

application/
   Bootstrap.php
   configs/
      application.ini
   modules/
      default/
         controllers/
         models/
         views/
         Bootstrap.php
      main/
         controllers/
            UserController.php
         forms/
         models/
            resources/
            validate/
         views/
            scripts/
               user/
                  complete-registration.phtml
                  index.phtml
                  register.phtml   
         Bootstrap.php
      rest/
         controllers/
            LoginController.php
         models/
         views/
         Bootstrap.php

Now to the problem. I have defined few actions within the UserController.php which I cant seem to access. For e.g. if I go to localhost/main/user/register I cant access this. However I browse to localhost/main/user it works.

I have no idea what it could be but my wild guess is its something to do with my Bootstrap.php. While debugging I commented the rest route initialize in the main bootstrap.php and it seemed to work. I have given the all the files that I think are affected by this. If I can know what it could be it would be awesome. Already spent like few days trying to figure this out.

Bootstrap.php

<?php

class Bootstrap extends Zend_Application_Bootstrap_Bootstrap
{
    // Commenting this seems to make the module auto initializing work.
    protected function _initRestRoute()
    {
        $this->_logger->info('Bootstrap ' . __METHOD__);
        $this->bootstrap ( 'frontController' );
        $frontController = Zend_Controller_Front::getInstance ();
        //$restRoute = new Zend_Rest_Route ( $frontController );
        //$frontController->getRouter ()->addRoute ( 'default', $restRoute );
        $restRoute = new Zend_Rest_Route($frontController, array(), array('rest'));
        $frontController->getRouter ()->addRoute('rest', $restRoute);
    }
}

Main/Bootstrap.php

<?php

class Main_Bootstrap extends Zend_Application_Module_Bootstrap
{

}

Main/controllers/UserController.php

<?php

class Main_UserController extends Zend_Controller_Action
{

    protected $_model;

    public function init()
    {
        // Get the default model
        $this->_model = new Main_Model_User ();
        // Add forms
        $this->view->registerForm = $this->getRegistrationForm ();
    }

    public function indexAction()
    {
    }

    public function registerAction()
    {
    }

    public function completeRegistrationAction()
    {
        $request = $this->getRequest ();
        if (! $request->isPost ())
        {
            return $this->_helper->redirector ( 'register' );
        }
        if (false === $this->_model->registerUser ( $request->getPost () ))
        {
            return $this->render ( 'register' );
        }
    }

    public function getRegistrationForm()
    {
        $urlHelper = $this->_helper->getHelper ( 'url' );
        $this->_forms ['register'] = $this->_model->getForm ( 'userRegister' );
        $this->_forms ['register']->setAction ( $urlHelper->url ( 
            array (
                'controller' => 'user', 
                'action' => 'complete-registration' 
            ), 
            'default' ) );
        $this->_forms ['register']->setMethod ( 'post' );
        return $this->_forms ['register'];
    }
}

application.ini

[production]
autoloadernamespaces[] = "Zend_"
autoloadernamespaces[] = "SB_"

phpSettings.display_startup_errors = 1
phpSettings.display_errors = 1

includePaths.library = APPLICATION_PATH "/../library"
bootstrap.path = APPLICATION_PATH "/Bootstrap.php"
bootstrap.class = "Bootstrap"
appnamespace = "Application"

; front controller
resources.frontcontroller.moduledirectory = APPLICATION_PATH "/modules"

; modules
resources.modules[] =

resources.frontController.params.displayExceptions = 1

resources.db.adapter = "PDO_MYSQL"
resources.db.isdefaulttableadapter = true
resources.db.params.dbname = "****"
resources.db.params.username = "*****"
resources.db.params.password = "*******"
resources.db.params.host = "*******"
resources.db.params.charset = "UTF8"

[staging : production]

[testing : production]
phpSettings.display_startup_errors = 1
phpSettings.display_errors = 1

[development : production]
phpSettings.display_startup_errors = 1
phpSettings.display_errors = 1
resources.frontController.params.displayExceptions = 1

Managed to get it to work by doing the following. Hope this will be useful for someone.

Created a route within the front controller plugin.

class SB_Controller_Plugin_Initialize extends Zend_Controller_Plugin_Abstract
{

    public function routeStartup(Zend_Controller_Request_Abstract $request)
    {
        $frontController = Zend_Controller_Front::getInstance();
        $restRoute = new Zend_Rest_Route($frontController, array(), array('rest'));
        $router = $frontController->getRouter();
        $router->addRoute('rest', $restRoute);
    }
}

in application.ini,

resources.frontController.plugins.Initialize = "SB_Controller_Plugin_Initialize"