Is this a new rope? Did you "unroll" it per the manufacturer's recommendation when you first flaked it out?
The way you or your partner is belaying can also introduce twists. If you're using an ATC or a GriGri off the belay loop, the rope should be aligned more or less vertically - you may have been taught to lock off with your brake hand at your hip, but holding it straight down is more effective. If you're belaying with an eight - well that's your problem right there.
At any rate, if you can find a place to let the rope hang freely for a while, like off the anchors of an overhanging route, that'll help get a lot of the twists out.