Could be motherboard could be cpu which has the memory controller in it.Which board,which cpu?
Seems like one channel isn't working fine,since no beeps with the stock cooler maybe that the cooler isn't tightend correct,to much pressure on one of the corners,you should tighten gently each corner a bit untel the cooler can't move or only just slightly.
Your cooler may be working with a crossbar,tighten each of the two screws just a bit until as described above.
Also maybe that one slot needs to be occupied at all times like the second one counted from the cpu.