If your store is not live yet. Follow this:
1) Empty/Truncate core_url_rewrite table from Database.
2) Disable Permanent Redirects from Magento Backend.
3) Reindex Catalog URL Rewrites and all your URL’s will be corrected.
very easy:
1. database backup
2. install remote mysql editor (like navicat)
3. find core_url_rewrite, then empty table
4. delete var/cache
5. reindex catalog index rewrites in index management
If you want to completely delete all url rewrirtes. This worked for me!
1. Login to phpMyAdmin
2. Click you databse name on the left
3. In the right window, click your database name again (up top) it will list all the tables.
4. Find the “core_url_rewrite\” table. click the checkbox on the left.
5. To the right, click Empty!
6. Login to magento, reindex.