As to why PS/2 keyboard won't work with a certain motherboard, there could be two reasons:
1) insufficient power
2) protocol violations - bad timings, signal integrity problems, etc.
Once a dedicated MCU, the motherboard PS/2 controller is nowadays buried in the Southbridge (if present at all) as a macrocell. So it varies wildly in implementation, and with the small firmware it includes, that's another possible source of problems.
Ripster, why don't you try further correlating the PS/2 problem with the Southbridge chip used? Like, two different motherboards using the same Southbridge chip (PS/2 controller)? Perhaps GHers could lend a hand.