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I thinks that's why I assumed it was the motherboard, because I had two sets of matching sticks working on one set of slots, but not in the other.
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From what you're describing, it definitely sounds like your motherboard. Good job by the way on the analysis of your problem.
I sincerely don't believe your RAM is mis-matched. Nor are the memory modules themselves (little chips on the DIMM sticks), As long as it's the same brand, series and timings everything should be fine, the voltage setting is through the motherboard.
You can put 2GB and 1GB sticks together on the same motherboard with no problem at all. I have done it my myself and my computer runs flawlessly.
In DDR2 or DDR3 RAM configurations the sockets are color matched, so as long as the 2GB stick are in the same color sockets and the 1GB sticks are in another color sockets your fine.