New box, memory problem

[compdoc]

> If I put one pair in 2&4 with 1&3 open, might that damage the MB?

won't damage it, but it might not boot or be stable. OK to try, though. Make
sure no dirt or hairs are in the memory slots.

When using the maximum amount of ram, not all boards support the maximum
speed the ram is rated for. You might need to set for a lower speed like
1600 before adding all dimms, and then try setting the proper speed. 

You can also try clearing the cmos after installing all dimms. Make sure the
slots you are calling 1&3 and 2&4 are shown that way in the manual.

You don't mention the cpu, ram speed, if the dimms are all the same brand
and model, or if the bios is the newest version for the board. 

A.6 is the last bios shown on the MSI support page. Updating the bios can
fix weird problems like these, but before flashing run memtest86 for one
pass.

I have also seen a sliver of thermal paste get under the cpu and stop a
pci-e slot from working in x4 or x8 mode. Worked ok with an x1 card, until I
figured out the problem. 

No reason something like that, or even a bent cpu pin couldn't cause this
problem.