The problem is that just copying the index.php file will not do the trick, because all the app/ folder etc is missing.

To get around this, in your index.php you need to set the MAGENTO_ROOT to be one folder up:

define('MAGENTO_ROOT', getcwd() . '/..');

Then it should work.

However, you also want to make sure that your skin etc is loaded from the parent folder, so in your Magento backend, you will need to enter http://mydomain.at/ instead of http://mydomain.at/en/ for skin, images etc in the URL management.

Hope this helps!

Be sure to set the default home page under Admin -> System -> Configuration -> Design -> Default Pages -> CMS Home Page. Change the Configuration Scope to each Store View and select the CMS pages that you've created for the home pages.

Edit:

Try this approach instead of .htaccess.

index.php

/* Store or website code */
$mageRunCode = isset($_SERVER['MAGE_RUN_CODE']) ? $_SERVER['MAGE_RUN_CODE'] : '';

/* Run store or run website */
$mageRunType = isset($_SERVER['MAGE_RUN_TYPE']) ? $_SERVER['MAGE_RUN_TYPE'] : 'store';


// New code 

switch($_SERVER['HTTP_HOST']) {
    case 'www.dist.c*****ment.com ':
    case 'dist.c*****ment.com ':
        $mageRunCode = 'wholesale';
        $mageRunType = 'website';
    break;
}

// end of New code

Mage::run($mageRunCode, $mageRunType);