bill1024
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.

Thanks for all the suggestions Bill, those are good options to think about.

Did you change your RTL?  That can very likely do it.

529th
Did you change your RTL?  That can very likely do it.

Hmm that's interesting, but no I haven't changed it. I have checked Boot Advanced Options for start up as well to make sure the settings are correct, but later discovered that the system won't boot with a single module in the #1 slot and will in the #2 slot etc. so, I'm thinking it's not on a software level.

I had a similar problem to this. The way I fixed mine was to fill the mem dimm slots in this order 2,1,4,3,6 and then 5. Don't know why this order worked but it did all 24GB shown and useable. Only problem that I have now is the memory control select is stuck to 2:10 even when 2:12 is selected in the BIOS 

Knightviper
I had a similar problem to this. The way I fixed mine was to fill the mem dimm slots in this order 2,1,4,3,6 and then 5. Don't know why this order worked but it did all 24GB shown and useable. Only problem that I have now is the memory control select is stuck to 2:10 even when 2:12 is selected in the BIOS 

You have me a little stumped on this. What was your procedure for filling the slots? I have all the slots occupied, but with only 2GB sticks for a total of 12GB. Also, Is the slot numbering you list according to the numerical specification in the manual or just starting from the CPU?

Starting from the CPU side (black slot) that's No.2 fill that first then the red No.1 slot, black No.4 slot, red No.3 slot, black No.6 slot then last red slot is No.5.
This is from the manual
Your new motherboard has six 240-pin slots for DDR3 memory. These slots support 256 Mb, 512 Mb, 1 Gb, 2Gb, and 4Gb DDR3 technology. There must be at least one memory bank populated to ensure normal operation. Use the following the recommendations for installing memory. (See Figure 1 on page 14 for the location of the memory slots.)

One DIMM: If using 1 DIMM (Single Channel), install into: DIMM slot 1.

Two or Four DIMMs: If using 2 DIMMs (Dual Channel), install into: DIMM slots 1 and 3. If using 4 DIMMs (Dual Channel), install into: DIMM slots 2, 1, 4, and 3.

Three DIMMs: If using 3 DIMMs (Triple Channel), install into: DIMM slots 1, 3 and 5.

Six DIMMs: If using more than 4 DIMMs, use: DIMM slots 2, 1, 4, and 3 then proceed to occupy the following DIMM slots in this order: 6 and 5.
 
I placed the dimms in that order and it worked for me

Wow this is sounds crazy. I understand concerning the amount and type of DIMMs used and the recommended slots. I'm assuming you have two matched sets of 3 DIMMs, which is what I have, so all the slots are occupied. Just to make sure I'm understanding this correctly, with the computer off, you had to install the DIMMs in that order, and then boot system? 

yes got 2 12GB kits so all slots are filled and placed them in that order then booted the system
 

Knightviper
yes got 2 12GB kits so all slots are filled and placed them in that order then booted the system
 

I gave it a whirl, but no luck. Thanks, though. Does anyone know of a cpu pin map available to check continuity? I realize I might go blind or mad attempting this.