do you have cpu-z instaled on your sr-2 rig?
i like to know if you can read all ram slots a the SPD tab.
and did you test all the rams?
like putting 6 dims in test if they work and than replace them whit 6 other thil you have don them all.
and if you fill all the banks and you disabeld 1 cpu whit the jumpers ,if you stil see the full banks or if ther also missing som rams.
i don't have experiance whit 12 dimms.only 6 ar instaled

Take it in small steps, we need to find out if it is the ram or the cpu's settings making it unstable. Drop the divider down on the ram to run it at a lower setting than stock, then do your tests, if it still is not stable then its the cpu settings and its time to work on those. You make a change at anything then test.

I doubt it's the cpu settings since even with bios all cleared and cpu's running at their stock speeds it still doesn't see all 48 GB.
 
Here's my cpu-z for ram: 

All slots are populated with the same as above.

the ram divider is the setting wher you can set 1333 , 1066 and 800

1.80V. It's also in screenshot. And I tried all dividers already. One thing that is or is not related is whenever I reboot Win'7 it never posts. I think the code I always see is FF or F4. I have to hold the power button to turn it off and back on again. Possibly a stability issue although the system has been running fine at 4.1 GHz full load for almost 9 hrs now.
 
Anyway, 40 GB is max I can get. Tried higher/lower dimm voltages. Not sure what else I can try.

The ram is controlled by each cpu, if you could only see half the ram I would say bent cpu socket pins bit since it is just some of the ram I would pull all of it and place one stick per cpu and test all of it to make sure it's all fine, then start adding ram until the bad slot is found if all the ram passed as good. The cpu temps are up there because of voltage, if you personally did not do the heatsink paste then re do it just to make sure, if you did do it then it must be fine.

cuda-dude: I decided to take your advice anyway even though it didn't make sense and here's what I found out.
 
Dimm slots on cpu0 all work and see 24 GB of the ram (6*4) at BIOS, OS, e-leet and cpu-z.
However, on cpu1, two of the dimm slots BIOS & OS won't see but CPU-Z/e-leet does and gives me the correct total ram.
 
So at post and in windows, 6 sticks of ram in all dimm slots on cpu1, it shows me 16 GB of ram yet if I load up evga e-leet or cpu-z they see all 6 sticks on cpu1, 24 GB total. How is that possible and what does that mean? If the two dimms are bad, why do eleet and cpu-z see them?

Makes sense. I looked carefully at the two dimm slots and although I don't have a magnifying glass around the dimms and the pins inside look good.
 
Next will be to remove the cpu coolers and check the cpus and sockets for bent pins and I have a feeling it'll be one of those. And if that's the case then I should probably just leave things as they are and be happy. But I know I'll keep thinking about it and sooner or later I may break and inspect them anyway. For now, I think I'll just leave it especially since I don't need that extra 8 GB of ram.
 
Man, I knew I should've inspected the cpus and sockets before paying but I ran a quick check and everything was fine. I knew it was posting only 40 GB but I figured it's because of the overclocking or that the ram timings needed to be set in bios. I didn't want to hold the guy up and play with the system for so long especially since he delivered it to me. Maybe that's why I can't OC higher than 4.1GHz too? 

Yes it was disabled with the jumper. I repeated the same test a 2nd time without disabling the cpu jumpers and same thing.
 
Other than that I'm still wondering if everybody else has their cpu1 run about 12 degrees hotter than cpu0, at least with the x5670's?
 

Closer than 12 degrees? I guess you mean less than 12.
 
Maybe someone else knows? Doesn't have to be with x5670's. Can someone else tell me what difference in temps they have under full load for cpu0 and cpu1???

Not much difference in temps in those pics. I found it odd though that the bios version in that pic is 080016 (same as mine) but the dates are completely off with it being 08/25/2011 while mine is 04/24/2013 although 04/25/2013 is the date shown on evga's website so I think I do have the latest bios.

Where does it tell you that id? Cpu-z somewhere? For the bios in cpu-z all I have is the version, date and brand.

I decided to remove cpu1 (I knew I'd do this eventually) and inspected the cpu and socket. No issues found. The only thing left to do is to swap the cpu's, cpu1 with cpu0 and cpu0 with cpu1, to see if it follows the cpu. I will do that later.