Yep - it's all to do with using the graphics card.
It's quite blatantly obvious but I'll state it:
If you are hashing on a graphics card and the card isn't doing anything else, you get your expected X MH/s
If however, the graphics card is ALSO doing something else, it will reduce the X number by some amount in relation to what extra you are doing.
Try running a 3-D screen saver
(of course if that something else is extremely small the reduction in X may be small or negligible also)
If you aren't seeing the above, then you are either not getting the correct expected X MH/s or you are confused about which cards are mining and which cards are mining + doing something else.