Settings seem way off for photos shot up to the sky... I seldom shoot clouds or sky at over ISO 100, except sunsets at times... Also, I think you should shut off some of your settings in camera, like NR in long exposures and the others that are similar... you have NR set to strong in one of them, I find standard more than adequate. Seems like your settings need some tweaking to me...

Your bird shot looks oof as well... you may want to try a different focus preset and bump your shutter speed up to at least 1/1600-1/2000th, then ISO 640 may be appropriate, but you won't have the noise issue... at the distance you were, you probably could have been shooting the bird at f/2.8 or 3.2... that would help too... I only seem to experience bad noise issues when I'm shooting low light and then it's mostly in the shadows, especially if I'm doing some portrait work. Daytime shooting outside is seldom a noise issue...
Good luck!
EOS 7D, EOS XSi, EOS 60D, EOS 70-200mm L f/2.8 IS II USM, EOS 100-400mm L F:4:0-5:6 IS USM, EF-S 17-55mm f/2.8 IS, EF-S 18-135mm f/3:5-5:6 IS II