Your first image shows a weird sun. I see the bloom and halo; but no sun. Is this a custom mission? If so, how many lights did you setup? Also, remember that backdrop objects like Planets act like light sources now.
Your third image clearly shows a Star Destroyer with a clear shading going from dark gray at the tip to almost white near the towers. So, shading is being applied. I suspect you've got too many lights, maybe?
@Trevor: Can you tell me which missions show flat shading? Try some skirmish missions to see if there are any changes. Also, try the Deferred shader to see if you have problems there as well (I noticed you have way too many samples for SSDO, we can come back to that later).