WordPress 3.1 went live yesterday which comes with many extremely useful features like inter psot linking, admin bar, custom post type etc. But for some upgrading to WordPress 3.1 turned out to be nightmare, many bloggers are reporting issues with permalink after upgrading to WordPress 3.1, from complete permalinks stopped working to partial issues like category & archive links stopped working & WordPress forum is flooded with such threads reporting similar issue.
Though few found out that following plugins causing issue which upon disabling fixed the Category & Archive stopped working.
Plugins Causing Permalink Issue in WordPress 3.1
2. Advance Permalinks Plugin
Few more steps for troubleshooting
1. Try disabling all plugins
2. Try changing permalink structure
3. Clear caches if you are using any caching plugins.
4. Regenerate htaacess file from WordPress Permalinks settings page, make sure to backup your existing htaccess.
WordPress team has not confirmed these issues & we are still unsure on how widespread is this issue, but we know there are numbers of users using facing issues after upgrading to WordPress 3.1.
Let us know in comments if you have found out any fix for category & archive stopped working after Wp 3.1 upgrade or facing some other issues after upgrade.