MacPro showing 3GB of 12GB installed on Snow Leopard

I have a MacPro3,1 that has 12GB memory installed (4x1GB and 2x4GB) and sometime after upgrading to Snow Leopard the system started only accessing 3GB. The System Profiler shows that all the DIMMS are present, with the correct size under the memory tab, but only 3GB in the hardware overview. I have installed a new copy of snow leopard on a separate partition, and this boots with the full 12GB, so there isn't a problem with the memory, as best as I can tell. How can I get the full memory back online on the original OS?

Usually just one pair of DIMMs will report half their size, yours seems like something I'd first do an SMC Reset.
Marginal RAM and seems like last summer we (Mac Pro owners and forum) saw quite a few.
Your Mac uses FBDIMMs. They run hot, so much so that Apple recommends waiting 10-15 minutes after shutdown BEFORE opening the side door to prevent sudden changes in air temperature. And many users boost the fans just 300-400 rpm to allow more air flow and prevent the temps from rising - the SMC can wait too long to kick in and easier to prevent in the first place.
Someone else had almost identical situation, on this forum (and not in Mac Pro section for Previous to 2009). So actually the first time I've seen someone say it was OS related. What can happen is in a RAM situation like yours, marginal RAM is causing the system to "go bad" and require reinstall due to writing data. Parity errors can also end up with corrupt files. A good reason to do preventative maintenance on a weekly basis with Disk Warrior.

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