I have stumbled across a problem that occurred after an auto-upgrade to 2.8.4.
In short, wordpress isn't writing changes I make to theme files on the theme editor, but it is caching those changes somewhere.
I add the word "blah" to my header.php from a remote location, and press (Update File). WordPress happily announces "File edited successfully".
But, if I refresh the page, "blah" is not present. If I check out header.php on the server, the changes have not been written to the file.
But, and here's the weird thing, if I go to wp-admin on the local server (yay for VNC) and check out the theme file there, "blah" is present on header.php.
This means, the changes are being saved in WordPress someplace, but are not being written to the file on the server.