Some people are reporting broken permalinks after the big upgrade to WordPress 3.1 – I can confirm I am one of “those people”.
From what I can see it appears to be an incompatibility with plugins that are playing around with rewrite rules using the “generate_rewrite_rules” filter hook or there abouts – probably brought about by a change in the core functionality for generating rewrite rules in WordPress in 3.1.
My permalinks issue was caused by the Top Level Cats plugin and I am not the only one – deactivating the plugin fixed the issue.
Looking forward to seeing how this one pans out.
I’m using WP No Category Base and it is working fine with the 3.1 upgrade.
Haven’t checked out Top Level Category plugin, but if they both just let you remove that extra word in the URL, then switch it up.
I’ve the same problem as you, but i don’t use Top Level Cat, so this is the problem after upgrade to 3.1
Thanks Evan, I’ll look to switch over to no category base tomorrow.
I had the same problem after the 3.1 upgrade. It was due to the Top Level Categories plugin. Thanks for this post, saved me hours of chasing down the problem!
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If this doesn’t solve your category/tag link list 404′s (pulldown and top level menus) when you have a custom permalink for Blog Posts, try this “action” function. It’s worked on every site I’ve tried (including multi-sites) WITHOUT having to tinker with .htaccess, change the existing permalink structure, or disable any installed plugins.
The problem is with 3.1′s canonical redirect. Sometimes, just disabling the redirect fixes the pblm. But, if this doesn’t solve it for you, here’s a more extensive alternative hotfix link. Just put the code in your theme’s functions.php file.
http://wpcodesnippets.info/blog/how-to-fix-the-wp-3-1-custom-permalinks-bug.html