Okay, I found a solution to this. My theme has a setup where i include a file that contains the featured post - snippet.
This was in my functions.php:
require_once('library/featured_post_snippet.php');
The featured_post_snippet.php contained this:
if ( function_exists( 'add_theme_support' ) ) {
add_theme_support( 'post-thumbnails' );
set_post_thumbnail_size(90, 90, true);
add_image_size( 'some_size', 1000, 9999, false ); //300 pixels wide (and unlimited height)
}
The setup above broke my featured posts when I activated w3 total cache.
When I moved the exactly same code straight to the functions.php, everything works okay again. Hope this helps, seems like a minor bug in w3 total cache.