I'm going to hazard a guess without seeing anything about your system configuration, that you're running a triple channel setup with three sticks of RAM.
I've had similar issues with my system (quad core Xeon, three banks of RAM, lost one third of my RAM without warning). The symptoms suggested that one of the memory slots had gone bad; confirmed by pulling the sticks one at a time and checking how the system reacted, and then swapping the memory sticks around to see if it was the stick, or the slot. Since then, it's been an on-again off-again problem, with my system currently running stable with all three sticks - but I still have an upgrade on order to replace the marginal part.
TL;DR: my guess would be either a faulty stick of RAM, or a faulty memory slot on the motherboard. Try what I did, outlined above - pull one stick at a time (with the system off!) and power the system up, to see what happens. Once you've isolated it to one slot or stick of RAM, swap the sticks around to try to figure out if it's the slot, or the stick. If it's the stick, it's a fairly cheap problem to resolve - just buy a new one to match the good pair. If it's the slot, you're pretty much up for a new motherboard (and/or system, if you can't get the same motherboard, or at least one that takes the CPU and RAM that you already have.)