Do you mean the bow wave and deck water animations? I have this problem too.
One thing I've done is to Alt-tab out of the game, open task manager, right click on sh5.exe in the processes tab and change priority to realtime or high. This fixed the stuttering bow wave and splash animations for me.
THe downside is you have to do this every time unless you can figure out the permanent fix shown here by DelphiUniverse.
http://www.subsim.com/radioroom/showthread.php?t=181797
For whatever reason I couldn't get it to work on my machine but the priority change does help for me.