This was posted in a resolved thread but i have opened it up as it has not been fixed for me.
I unlike a lot of people am still having issues with the wp 3.1 permalinks.
I heard from users that categories ( the_category() in the loop ), post linking ( the_permalink() in the loop ) from index and categories sidebar ( using wp_list_categories() ) bring up 404 pages. I am using the custom permalink structure of /%category%/%postname%/ (which i thought was the most popular way, and featured on the wp help page).
What I have done so far:
– Started off by doing a clean install (new db, new folder on my dev server). Downloaded wp 3.1 and installed it in the new folder via my FTP client. Did the normal setup that i do all the time (100s of times before). Things were functioning from a wordpress standpoint except for the stated issues above (category and post pages getting 404s).
– So since it was a clean install there were no plugins that might be causing the permalink issues. But i went ahead and deleted the two default ones that come with WP 3.1 just to make sure (even though they were still disabled). Still getting 404s.
– So then i proceeded to do the suggested .htaccess delete and respawn action. Did this as described by many sites and still had the same issue. I did this like 10 times.
– So i was starting to think it was my theme… So i turned off my theme and reverted to the default (twenty10 theme). Keeping my permalinks set to /%category%/%postname%/. The same issue was happening with this theme. So this is what made me think that it was not my theme and more of a WordPress 3.1 issue.
– If i set my permalinks back to default, they of course work fine, but i have thousands of people using my theme and use the custom permalink structure. So I am afraid that those people are a.) going to have broken sites if they upgrade and b.) have broken links if they revert to the default permalink structure.
– I tried to install the hotfix plugin and that did nothing.
– I made sure that my code was not chaining permalinks like some of the plugins that were causing the issues. Nothing there to cause my troubles…
The only other step that i have not done was install another instance of wp 3.1 in a completely different folder on my server… I was saving this as a last effort if there wasnt a fix that someone uncovered.
So that is where i am and what i have done. Hope that this is clear and links you to a possible solution.