Yes, it is very strange. If I turn off 3D clouds it's smooth as butter. Something specifically related to the way the clouds are rendered seems to cause the strange behavior.
As for mods, I've got a pretty good list going.
Ailclouds 3.0
Accurate German flags
ailimpurity light
ailmoon 1.5
ailwhiteinterior
BaRF 1.3
Doom's Decks
Interior working dials
Mighty fine crew
More crew commands by dialog
More realistic periscopes
No crosshair
No bubbles/halos
Remove login intro movie
ailrain
digital clock
stadimeter fix (with clock patch)
Damage assessment
No surface hydrophone
I've also just tried it with stock clouds and the behavior is still there. I'm pretty sure it was there from the beginning before I added any mods at all. Nothing I've done (v-sync, AA on/off, resolution, mods, affinity, priority, etc) has affected the behavior. Fortunately it's not too noticeable from on board the boat, but if I want to look around with the external camera I'm going to notice it alright.
