[archer]

If you have an ATI card, Go to your Conf.ini and search for Water=X (x being what ever number is there most likely 1) and change to Water = 2.

If you have an NVidia card go change it to water = 4. Set weather to anything worse then Hazy and you will see waves. YOU MUST AVE GRAPHICS ON Perfect

I also see some waves with clear weather when I have my water=2 on ATI, but when weather is worse there are a lot of waves.
But when I have my water on =2 the game will crash within 30 seconds, it plays fine, till I fly low over the water or when I look down.