Interesting. I commented out the disableProtection() function, but my keys just got wiped again and spam started to come in. Any idea what else could be causing the keys to vanish?
Updated to 3.89, while this fixes the boxes display, it seems the look has changed? Is there a way to change it back (e.g. show stars instead of text)?
Edit: The latest downloadable copy for 3.2.0.1 still seems to have missing files. Hitting the same Error 500 on updating via WordPress. Will roll back to 3.1.9.1 again.