Two sets of memory will load the memory controller more than one set - the bios will usually default to a reduced speed to accommodate this behavior. You might be able to set the higher speed in the bios, but I would run a memory test to be sure.
Does the full memory capacity get recognized? I've seen cases where a memory module didn't work because it wasn't completely seated. As a sanity check, make sure that each pair of memory slots comprising a single physical channel has memory modules of the same type. You could try pairs of memory modules by themselves. Finally, there are bios settings (ganged/unganged and dinterleaved) that might make a difference.