OK, looking at the image on the download page (that's all I've got to go by) Slots DDR3_1 and DDR3_2 are the two slots nearest the CPU. If your RAM Modules are in these then either the numbering on the motherboard is incorrect or the way that the software is reporting them is at fault.
Are you running the F5 BIOS? If yes, does it report the memory modules in correct slot if you use earlier F4 BIOS?