Is it likely? All the memory modules are good. I don't see any bent CPU pins.
 
If on module is installed in the 1st slot for triple channel, it is recognized and utilized by windows Edit: it no longer boots with only 1 stick in the slot 1
If I install two more modules the 1st slot is recognized, but is in Hardware Reserve unused
If I populate all the slots they are all recognized, but the 1st slot and the one next to it are in Hardware Reserve
If I remove the 1st module and the one next to it, the remaining 4 modules are recognized and utilized with a normal amount of Hardware Reserve.

You say none of your pins are bent so try some of the steps here in this old troubleshooting guide of mine. Although this might seem to be unrelated many of the steps here have helped forum members with the same issue you have currently: http://forums.evga.com/FindPost/479626

Might be worth a try to just reseat the cpu a bunch of times. I was having the same symptoms you are describing and I had to reseat my X5670 6 or so times for it to detect all 24GB's of ram that I had installed. 

Thanks RJ, but everything checks out with the guide

tucker147
Might be worth a try to just reseat the cpu a bunch of times. I was having the same symptoms you are describing and I had to reseat my X5670 6 or so times for it to detect all 24GB's of ram that I had installed. 

You had to reset for the ram to be detected? but in my case the memory is seen just not usable. I know this from task manager/resource monitor/memory and the above scenario of installing the modules. I have a total of 12288 MB installed, which is correct, a total of 8183 MB, and 4105 MB is Hardware Reserved, which is basically 2 modules of memory. I have two sets of matched memory and I have made sure when testing it the sets are installed in sequence accordingly. I have read a bent CPU pin can cause this, the module is detected, windows puts it in Hardware Reserve because there is no communication with memory controller, but the pins look perfect....Hmm maybe the cooler screws aren't tight enough. OK you talked me into it, I'll try resetting it.

Rechecked my CPU and downloaded this Intel Processor Diagnostic Tool. The test said it was good. Would this be a conclusive test for IMC? It sees all the memory installed. I rechecked the memory modules and found that with just one stick installed in slot 1 it will not boot, but it will boot from slot 3 or 5. If all the memory is in all the slots accept slot 1, there is still one module in Hardware Reserve. If I then remove the stick from slot 2 all the remaining memory is being used with the usual low amount in Hardware Reserve. So, with memory installed in either slot 1 or 2 it just sits in Hardware Reserve and does nothing but look good. Processor or MOBO? This guy made a great vid, but I can't see anything obviously wrong. Any ideas? 
 

ILikeBeans
Rechecked my CPU and downloaded this Intel Processor Diagnostic Tool. The test said it was good. Would this be a conclusive test for IMC? It sees all the memory installed. I rechecked the memory modules and found that with just one stick installed in slot 1 it will not boot, but it will boot from slot 3 or 5. If all the memory is in all the slots accept slot 1, there is still one module in Hardware Reserve. If I then remove the stick from slot 2 all the remaining memory is being used with the usual low amount in Hardware Reserve. So, with memory installed in either slot 1 or 2 it just sits in Hardware Reserve and does nothing but look good. Processor or MOBO? This guy made a great vid, but I can't see anything obviously wrong. Any ideas? 
 

Sounds like the motherboard is the issue.

I bought a E5640 for cheap to test it. Wondering if I'll have to do the QPI mod.

Got my $15 Xeon and did the Westmere mod! (thanks for the pics Tucker147) It booted it up and.... it must be the MOBO same problem. Such a shame, I have a brand new unused EK full cover chipset block for it too, not to mention the 980X. Never had the chance to upgrade it...
 
Anyone know what component might have failed? I figure the socket might be good sense windows seeing the RAM installed.  

That stinks. But at this point if you can not fix it a couple things come to mind.
 
With the 980x and a set of G.Skill 2x8gb of 1866 memory, it is dual rank ram, dual rank in dual channel should be close to triple channel, single rank memory.  Sell your 12gb kit and get a 2x8gb kit... Use as is, 980x dual channel ram. I am running an Asus Rampage3 with a bad ram slot, with x5660 and 2x8gb G.skill 1866  it runs just as good as my other X58 boards in BOINC primegrid and WCG
 
Or Sell the 980x, they are still selling for around 200$ +- or so on Ebay, sell the board as "broken" and say it works, but has "These problems" will take Westmere CPUs. Look for another board.
 
Sell it all and upgrade to the X79 platform and get a cheap E5-1650 xeon hexcore for 100$ or less and go that route. Reuse your memory and all other parts.
 
Or even upgrade to the newer Haswel CPUs. Can still use your DDR3 and the rest of your parts. Should not cost to much more than you will get for the 980x, the e5640 and motherboard.