The Corsair part number CMY16GX3M2A2400C11R is for a single kit of 2 sticks, total 16GB. That pair should work in slots A1 and B1 (check the M6E manual, it might be A2 and B2). In my experience, the Haswell IMC (integrated memory controller) is good enough to handle about anything in the 2400MHz range.
A systematic way of troubleshooting is to try one stick at a time and try it in each socket. Be sure that one stick is fully seated. In this case I expect to get the same result - good in channel B, but not in A.
A common cause of one bad channel is that some CPU socket pins are not making contact with the pads on the bottom of the CPU. I suggest removing the CPU, checking for bent pins, and reinstalling the CPU. Be sure to tighten whatever cooler is used only enough to be in firm contact with the CPU. Too much cooler pressure is one cause of socket pins getting misaligned.
Another possibility is that the CPU is bad. I have one like that (with no warranty since it's delidded) in which channel A memory doesn't work. It is also possible that the motherboard has a problem. Did the PC ever work? In what combination? Do you have another CPU to try as a means of assigning fault?
Jeff