I keep seeing this efect the sea surface in 2.0. I'm not sure if this is caused by GWX 2.0, my AGP card or the drivers. I can't recall it being there so much in 1.03, but having changed my AGP card with the release of 2.0 I'm not sure of the cause.
Sapphire X1650 Pro,
Omega v3.8.291
AMD 64 1620 LE
X2 1Gb DDRII 800
(Game profile for SHIII/GWX : AA6, AF4, texture preference-high quality, mipmap detail level-high quality, v-sync-application preference)