What motherboard have you got? It sounds as though you've got a dual channel option, though to use it you have to use pairs in certain slots - alternative configurations may not work which would explain your problems.
Consult your manual and see what it says - My motherboard, for instance, has two banks of two DIMM slots - one bank can be used with any combination of RAM modules, the other is dual channel and therefore requires two identical RAM modules to function properly (possibly at all).
Have a look at the manual or find out what board you've got and we can probably give you more information. There may also be a jumper on the board, though without knowing more I can't really tell you.
One thing you could try is to use slots 3 and 4 (If you have that many) - Slots 1 and 2 on my board are the dual channel bank which I don't use.