jonradio on "Pre-existing subdirectory install"

Try saving Permalinks. Don't change them, just hit the Save button in Settings-Permalinks in the Admin panel.

To clarify, these are the instructions you "should" have been using:
http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory#Using_a_pre-existing_subdirectory_install

In other words, that's what works best for me.