This is a known bug with the acceleration cache. Turn off the acceleration cache in the quality tab for the cloud layer and it will go away.
Edit: oggyb, you were correct about the cloud layer. You set the altitude of the middle of the clouds, vertically; the bottom of the cloud layer is at (altitude-depth/2), and the top is at (altitude+depth/2). Taking njen's example, the lowest parts of your cloud will actually be at 750m, and the highest parts at 1250m.