Ok, we had this issue in previous version of WP, there was a bug about rewrite issue.
We reverted back to previous version, and all was good. We were on sub-domain, finishing up the site.
Today, we switched all URLs to the top level domain and everything worked fine. Then, all of the sudden pages and posts stopped working. BUT, custom post types work just fine.
It uses postname setup, default urls work!
I tried resetting htaccess, resetting permalinks, changing themes to 2011, deactivating plugins, nothing works. I'm stumped.
I upgraded to latest WP, 3.4.1 which supposedly fixed the rewrite bug. Still does not work.
We've tried going back to previous version again. That did not work. So, then, all of the sudden permalinks began to work. 2 days later, they stopped working again!!
Please help! Out of ideas.