I have the same problem (It doesn’t go in any order except alphabetical), but I am using the default theme.
@ecographic, well it didn’t fix the iframe problem though. Oh well. Thanks for fix.
Nevermind. Sorry, I foudn my error. The .htaccess was not writable. I didn’t scroll down far enough to see the error.
@incrediblehelp, So make sure that your .htaccess is CHMODed at least 666.
I am having the same problem except that I am using one of the predefined “Date and name based” permalink. So, whether I try to goto posts/pages/categories/archives it will always give me a “The page cannot be found” error.