Pretty URLs not working after upgrade

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I just upgraded a site from 5.3.1.1 to 5.3.3.1 (and yes, I upgraded to 5.3.2 and 5.3.3 in between) and suddenly all pretty URLs are redirecting to the Home page. I can't see why that would happen … my rewrite rules haven't changed.

For instance, mysite.com/page1 redirects to mysite.com instead of mysite.com/index.php/page1.

Anyone else experiencing this?

Benji