This is a bit on the technical side but I believe it has to do with the 5000 series only having two TMDS's circuits that allow for DVI and HDMI to transmit their Digital signal. Obviously since their are only two of these TMDS circuits only two out of the three DVI/HDMI outputs will work. (why ATI decided to only put two TMDS's on is beyond me)
VGA and DP use something else (I have no Idea what they are called). Apparently if you use a DP to VGA adapter on the DP port it will force the card to use a RAMDAC circuit, thus allowing you to use three monitors.
Most of this info comes from this thread:http://www.tomshardware.com/forum/279385-33-success-eyefinity-passive-adapter
TheGreatGrapeApe takes all the credit.