If you're using these 2 tools together, you have to make small effort in order to get rewriting working properly. 

1. Do what it says here
2. Open wp-includes/classes.php
3. Go to line 158. You should see something like $req_uri = $_SERVER['REQUEST_URI'];
4. Replace that with $req_uri = $_SERVER['HTTP_X_REWRITE_URL'];
5. You're good to go!