I've seen this for awhile but is the rain suppose to pass the clouds since if you toggledownfall or it automatically rains, the rain is still going pass the clouds. Scientifically rain comes from water vapores over time then it becomes a cloud. Rain doesn't come from the sky unless this is one of those sky boxes...
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this is intended bhavior. there is a discussion in the forum on this, though it is not "scientifically correct", but it's not a bug.
to understand this: the rain is not related to the clouds in the sky but the player itself. it generates some blocks above him, even if he is over or in a cloud. look up this post of notch himself explaining it: https://twitter.com/notch/status/130230769347067905
As you can see, since all clouds are in the same height level, there are no clouds above the pre existing clouds in minecraft.