Optical Flares should render in front of the clouds, shouldn't it? The obscuration layer only obscures the light source. If part of the light source is showing, then the flare will appear on top of everything - exactly like the lens flare in a camera lens. If the source is obscured, then the lens flare will disappear.The question is therefore, how dense is your cloud? Is it dense enough to obscure the light source?
You could also try pre-composing the cloud layer. There is the idea lurking at the back of my mind that the obscure layer takes the layer’s alpha values before any effects are applied. Could that be the problem?
-f.
Thanks Felt, you help me a lot for my next move 