I\'ve imported 6K categories and 16K products to magento using a custom import profile. When I\'m trying to reindex everything works except for \'Catalog URL Rewrites\' that kee
You need catalog URL rewrites to make your catalog work properly. How long are you letting it run for? There's a really substantial amount of data to be written to it...
If you cannot make it work programmatically, it may be possible to shove the data into the table manually and force the index to feel refreshed? Caveat emptor, I have not tried this.