looking the specs over i think i have an idea what is going on. the mobo has the Q65 express chipset on it. according to intel's spec sheet for it, there is only support for x1, x2 and x4 pcie 2.0. with a max of 8 pcie lanes total. so the x16 slot is really not a x16 slot and therefore did not get the full x16 power supplied to it.
http://ark.intel.com/products/52811/Intel-Q65-Express-Chipset
i would guess it is at best a x4 slot and therefore was only supplied with the lower power needs of an x4 slot. if you look on page 29, it lists the hd 6350 gpu you could get with the pc as a max of 20w. this may also be a reason why the slot did not get full power as they never sold it with a gpu that needed it. pre-built systems are notoriously...