As I found out earlier today, after trying to replicate the environment in PHP dev as I have via cPanel, you do not want to use –prefix=/usr at all. I had both the /opt/phpdev directory and the /usr directory as prefix tags and evidently I did not see it. It ended up breaking the 5.3.8 install until I was able to recompile the proper paths in cPanel.
As a side note the new dev version currently usable on the server is PHP 5.4.0 RC2. Again contact me for details on how to prepare for the new version upcoming. Thanks!