obviously if they only work in slot 2 and 4 then it matters .
I assume you mean "am I loosing much for placing them in those slots". The answer is you shouldn't, it should work the same no matter which pair of slots you place them in.
but it really depends on your motherboard. And your motherboard has already proven problematic (in that it will not reboot if you have them in slots 1 and 3).
Best thing to do in your situation is to benchmark it yourself.
PS. check for motherboard bios updates, those CAN solve issues like the one you described.