I don't know if this helps but it kind of sounds like the motherboard DMI pool was not updated when the memory was first added and was never refreshed. To fix you have to trigger the BIOS to flush its pool and build another database. Often you can do this by making a hardware change, such as moving a hard drive cable to another port, disable some hardware and then re-enable it. Be sure to select plug and play OS in the bios if you have that setting. Some BIOSs will have options to rebuild the DMI pool, some have utilities you can run. bugs in BIOS versions also prevent proper hardware detection.
- you know that the BIOS plans to build a new DMI pool if you make a change and tell the system to reboot. if the BIOS has to build a new DMI pool, it should force a shutdown that acts like a cold boot rather than a warm boot.
-you could also have a physical problem with the interleave controller in your CPU or where it connect into the CPU socket.
- you could also reduce your memory speed and see if both RAM sticks are correctly detected. Each stick of RAM will cause a capacitance induced timing delay in the circuit. you can have both sticks individually run at 1600MHz in either slot but fail when both slots are in use. (generally, the timing is close, it works while the circuit is cool and fails during use later) low probability of this error in this case but check the lower speed just in case)
- first step would be to get your BIOS to work correctly without involving the OS.
- maybe have your BIOS do full tests rather than the default quick boot tests and see if that detects and updates your memory count in the BIOS
EDIT
- since you can run windows, try and download and run CPUID CPU-z program and
have a look a look of how it reads your memory bank configurations and see if they are as you expect or have set in your BIOS