1/ I remember there was a recent thread on 6600 or 6800 cards and the issue was resolved (search 6600 / 6800 resolved / solved and you'll find it ; make sure you check to search both words). It's pretty complicated though.
2/ Although a lot of people have tuned up their SH3 resolution, I wouldn't push a game that was not initially designed for that. At least I wouldn't expect to run flawessly.
3/ These are the finest graphics I've ever seen on a subsim. No offence for Dangerous Waters, but it looks like SH2. Nice gameplay though, and a lot of options. Imagine like you had an SH3 and be able to command XXIII, U-cruisers, XIV, milk-cows, mine-layers, V&Ws, Swordfish, Liberators and harbour AAs.
4/ If you ininstalled then re-installed and you still having problems, it's something that it remains in either your registry or /windows / system /whatever folder apart from /program files / ubi etc.. Remember what you installed in the past and get rid of it.
5/Be patient. This is a virtue of a real Kaleun