Hacked permalink structure 404ing

For the past few weeks I’ve been running 2.5 happily with the old hack to remove the category base from the permalink structure (empty the box in permalink settings, remove the ‘category/’ from rewrite.php) and my post permalinks set to “/%category%/%post%/”

It’s been working perfectly, beautifully in fact.

I had the following structure:

http://spencerlavery.com/ – homepage
http://spencerlavery.com/blog/ – top-level cat
http://spencerlavery.com/blog/the-cult-of-the-mac/ – post within ‘blog’ cat

http://spencerlavery.com/design/ – second top-level cat
http://spencerlavery.com/design/website-phobea/ – post within ‘design’ cat

http://spencerlavery.com/about/ – page
http://spencerlavery.com/about/spencer/ – sub-page of about page

Like I say, they all worked fine. Then today, I’ve done nothing but add a couple of new posts and boom, every post is 404ing.

Cats are coming in fine, but all posts are 404ing. Adding category base back in fixes it, but messes up my URLs (SEO) and my logical URL structure.

If anybody has any ideas on how to get it working again I’d be forever in your debt, I’m pulling my hair out over here.