posts not found after upgrade to 2.5.1

I just updated to 2.5.1, and I’m having a weird problem with my blog. It seems the blog is unable to find where my posts are in certain situations.

If you go to my blog, you’ll see that it gives a “not found” error for archives, pages, permalinks, etc. However, if you click on one of the categories in the sidebar, the a summarized version of the posts show up.

In the admin panel, when I go to Manage >> Posts or Manage >> Pages it gives a “not found” error. However, I see it give an accurate count of the types of posts such as “Published (260)”.

Again, when I go through categories it can find them. Manage >> Categories >> Posts (the count for that category) shows the list of posts for that category and I can edit from there.

Can anyone help me figure out what’s wrong. I am using a custom permalink style, but it is the same as from before the update. Thanks in advance.