Lodar,
I had the same problem with permalinks and the calendar and found following solution:
open the template-functions-links.php file in wp-includes directory, and change line 172 from
return apply_filters(‘day_link’, get_settings(‘home’) . trailingslashit($daylink), $year, $month, $day);
to
return substr(apply_filters(‘day_link’, get_settings(‘home’) . trailingslashit($daylink), $year, $month, $day),0,-1);
I also had to add “Options +SymLinksIfOwnerMatch” to the top of my .htacces file
