Ok, this was driving me nuts too as it seems to be completely undocumented However, fear not for it is surprisingly easy to fix! 😀
In your tiny_mce_before_init hook function right before the return statement simply add the line:
unset($init['preview_styles']);
This will make wordpress function as it did before the 3.6 update (the updated added a line in wp-includes/class-wp-editor.php [#347] which changed the default behavior.)
From what I can tell, this setting limits the css properties that will be previewed in the styles drop-down menu. As of 3.6 it is set to 'font-family font-weight text-decoration text-transform' by default. Thus causing properties like: color, size, line-height, etc. to not render.
So if you don’t just let everything slip trough you can also just add some specific properties to the list of allowed properties:
$init['preview_styles'] .= ' background-color color';
I know it’s a bit late, but hopefully this will help in the future since, as of 3.6.1, this is still the default behavior.