Why would an upgrade change all the settings?

A couple months ago, we decided that on a single machine, outside our regular development/staging/production environment to setup upgrade to PHP5, so I could test all teh sites, fix any problems, before we go ahead and upgrade all the machines.

I've been so busy since then, only yesterday did I get a chance to glance at the upgraded server. Turns out.. they installed PHP5, and went ahead and disabled mysql, oracle, pear, gd and well.. everything else.

How would I ever possibly be able to use this as a web server running data driven sites?? When I say "upgrade" I usually mean "Just like it is, except the newer version".

I've sent off the email to ask them to actually configure it in the same way as all the other servers, lets see how long this takes before I crack and do it myself.