I had this problem today on one of our sites that has anonymous access enabled. We wanted to link to some PDF files in our quick launch navigation, so, naturally, we logged into the site and manually added the links.
However, when we tested the site with anonymous access the links weren’t there! So, next step, check the document library. It was inheriting permissions, and I could even manually type in the URL to the document library and the PDFs using anonymous access and view everything just fine.
So, time to start digging. Fortunately I found a thread on a discussion board that pointed me here – http://support.microsoft.com/kb/927082/en-us?spid=11373&sid=200. Apparently when you turn on Anonymous access, Microsoft doesn’t think you could really want everything to be anonymous access. Anywho…I figured it was worth a shot, so I logged into the server, disabled the feature running the command in the KB article linked above, turned anonymous access off and back on and what do you know. It worked!!!
So, if you are having any trouble with certain lists, documents, navigation, etc. Give this solution a shot. As of yet I’m not aware of negative impacts to disabling this feature, but if I find any I’ll definitely update this post.