There may be quite a few reasons for stuttering under time compression: you are near land, theres a lot of traffic nearby, or maybe even a convoy (the game usually does that - stuttering with TC when heavy traffic or port is nearby - you can exploit this when hunting
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Other reasons may be - no matter how strong your PC is - its hard drive or partition with SH4 - may be fragmented, or there is something running in background and using your CPU (like antivirus software starting a scheduled scan). It's also a good idea to patch SH4.exe to use more than ~2GB of system memory (post your sys specs if you want help with this; [edit] and operating system (x86 or x64)).