I figured it out.
For the reference problem was links in custom post types. As it appears Qtranslate in its current iteration doesn’t support custom post types. And the_permalink or get_permalink will not change to current lang as you switch them.
Solution was very simple.
Just include this in functions.php file of your theme.
add_filter('post_type_link', 'qtrans_convertURL');
cheers!
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