I have stripped and sanded a window ledge from varnish, putting white primer on but turns yellow? help?

I don't know what you used for a primer but I would allow 48 hours drying time then lightly sand and prime again.The yellowing is most likely pigments from the wood bleeding into the primer. The long drying time will lock the pigments into the primer. The second coat of primer will seal them in better. After another 2 day drying period, its ready for the finish coats.