Ok, I finally found out about the uggly billboards. In fact, Atmosphere option of the Sun lamp is not friend with ZTransp alpha mapped planes... I will fill a bug report as I guess it is one...

But as I don't want to wait for the bug to be corrected, I messed with Composite nodes to correct this. I set up three rendering layers:

  • one with the clouds alone, Sky option deactivated
  • one with the sky alone
  • one with the landscape itself

Here's the nodes setup, based on the three previous rendering layers: