Happens in stock game usually when there are a lot of things for the game to keep track of. I get it most often after sinking an entire convoy, the game continues to process all the life boats, rafts, floating boxes and barrels until I'm 20 or so miles away. Some mods aggravate the effect, thinking there wasn't enough debris after a ship went down they edit \Data|Library files debris.dat and LifeBoat&Debris.dat to double or triple the amount of floating junk after a ship goes down. Looks great for 1 or 2 sunken ships, sink half a dozen and the game slows down because it's tracking all that movement.
If it's not related to a recent sinking (if the game doesn't smooth out when you're 20+ miles away) or near something that appears as a contact 5-10 minutes after the stuttering starts, check your video and sound drivers. Never figured out why, but unless the sound card can process audio correctly it somehow makes the video stutter even if the video card and drivers are perfect.
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