Hey, just for you to know, the aticonfig tool is broken. It never displays clock for me if more than one card is present.
Also, to your problem with only two cards working: be sure to run aticonfig after you added a card. Is the third card show in lspci?
I recently had problem with version 12.3 of atidrivers, that aticonfig --adapter=all created xorg.conf for three cards on machine with only single card. I needed to delete the other two by hand. That leads me to an idea, that you could try to add your third card manually:
In /etc/X11/xorg.conf should be something like:
Also, lspci says:
01:00.0 VGA compatible controller: ATI Technologies Inc Juniper [Radeon HD 5700 Series]
Notice, that the BusID is actually the same number what lspci says. Just create a third "Device" entry in you xorg.conf with third pciid and see what happens.
Note that this will only work if your problem is faulty aticonfig, as it was in my case. If your card is not even shown in lspci, the problem will be somewhere else. I've heard stories that some server boards have modified something that makes them not to accept graphics cards... Or simply there is something wrong with your third slot. (You may try 1x->16x rieser, even in your 16x; it could still help if there is short in some other pcie line)