If you're using these 2 tools together, you have to make small effort in order to get rewriting working properly.
- Do what it says here
- Open wp-includes/classes.php
- Go to line 158. You should see something like $req_uri = $_SERVER['REQUEST_URI'];
- Replace that with $req_uri = $_SERVER['HTTP_X_REWRITE_URL'];
- You're good to go!