First of all, welcome to Subsim, where the people tank always has room for one more.
I've found that most time compression stutter comes from all the targets in your sensor range, even the friendly targets. Time compression will also lag for a couple of seconds if you advance it quickly from 1 to 2048 or above. It seems like the game is doing a few housekeeping tasks, clears the memory and then the time compression takes off with great vigor.
Now you have a better processor than my Opteron 175 and a slightly faster vid card than my nVidia 7600GT. You should be charging around at 4096 or higher and not even worrying about it.
How long has it been since you defragged the old hard drive? That will make a major difference. You can get lag from background processes, especially instant messengers, update checkers, virus scanners, spyware turning your machine into a zombie, etc. Background Internet access is also a load you can do without. Rebooting if you find the game going slow helps almost all the time.
In spite of the fact that SH4 is not usually thought of as being in the current generation of resource hogging games, I've found that its demands are very high compared to some games that are traditionally thought of as resource hogs.
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