Sky in the distance dims when there is shade overhead. This is the opposite of what human eyes perceive; if the immediate surroundings are dark, sky in the distance should appear brighter. The brightness of clouds relative to the sky also alters.
Also applies to a lesser extent when swimming on the water's surface. Is the brightness of distant sky based on the light level at the player's feet?
I've used a mod pack which introduced a bug like this into a previous version, but it was worse. It was so creepy and disorienting I stopped playing that mod pack just because of it. It's not so bad in regular Minecraft 1.8, but it's a little disconcerting, especially when swimming in open water. It's very much the opposite effect you'd expect from days at the beach.
Environment
Linux
Java: jre1.6.0_30
CPU: Intel core 2 quad Q6600
GFX: nVidia Corporation GF116 [GeForce GTS 450] (rev a1)
Your Java is highly outdated.