The Eldar and Ork gods are a relult of the respective races beliefs and the effects they had in the warp.
One theory I have heard postulated, and even considered at one point, is that the eldar gods are in fact the old ones themselves, but there is too much fluff to contradict this.
The Eldar gods became the focus of the Eldar`s worship and devotion after the Old Ones civilisation collapsed. After the c`tan went into stasis, the eldar claimed the galaxy. At this point, they were the dominant race and their gods so dominated the warp. The chaos gods undoubtedly existed at this time, but three did not have the same level of influence they later would and the fourth lay dormant.
With the fall of the eldar and the birth of Slaanesh, the Eldar gods were destroyed (or whatever) and the chaos gods able to achieve true dominion. At this point, the Great crusade had begun and Mankind inherited the galaxy, bringing the threat of Chaos with it.
The ork gods of course, are simply the epitome of orkish belief. Their influence ultimately is not deemed a serious threat to the four powers.
EDIT: Ninja`d by CotE. Should have known.
EDIT: And Ninja`d Eddy!