I too had this psychadelic color problem, but i only noticed it when i initially installed GWX. It happened once when i submerged in the kiel canal. I closed SH3, restarted my computer and it never happened again, ever. 4 months ago i built a new computer, with new cards and have only had one odd periscope issue. It occurs once in a blue moon and only to the attack periscope. when i raise the scope, the blurriness of water running down the lense wont stop, it is like an infinite supply of water is running down the lense... the only way to correct this is to surface the boat and raise the attack scope all the way up, leave it up and submerge with it up. this happens so rarely that it is not even annoying. just one of those "oh well, ill just use the other scope" things.
The only advice i can offer you is
make sure that you are using the latest drivers. If that doesnt help you might try to revert to the previous drivers if that is even something you can do.
if that doesnt help i can only say that the Nvidia 8800 series cards are very nice
