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Just something you might want to try.
Because if you don't it is usually a good first step when having FPS issues in games.
I used a program to measure my CPU load while I play and according to it no core went past 50% usage while playing, yet Steam overlay said I was getting only 30 fps and the stuttering was still happening.
Try to deactivate Steam Overlay, might help you in that Case then.
Other than that, there are FPS Boost mods available for Factorio that might help in your Situation, just check the Factorio Forum.
So maybe check your monitor settings if your monitor is more than 60hz?
I've noticed once I complete all the tasks in the upper left the game turns buttery smooth and the stuttering stops. What's causing that?
@Renda: Maybe you should report this on the official forum, after AlexMBrennan's test it could sound like a bug.
Find it at forums.factorio.com
Windows may also mess up some games with power saving settings. It might have even been problem with Factorio for some users. Basically if a game uses so little CPU the OS may think it can reduce the CPU power and then it overshoots... then ups it back again and you see that as stuttering. Such things can be turned off.
Added discussion to bug reports:
https://forums.factorio.com/viewtopic.php?f=226&t=85243
The script update is particularly bad since the first and second columns are both significantly higher than what you would expect.
I went and downloaded the demo (from the factorio website but it should be the same as the one on steam) and after progressing though it somewhat close to where you were here is what I have:
https://imgur.com/M70JP0G
As you can see the numbers are all significantly lower than yours, and while I have a pretty good computer (AMD Ryzen Threadripper 2920X and NVIDIA GeForce RTX 2080) it isn't to the point where it could make that big a difference.
It seems like your computer decided that factorio isn't worthy of getting a core for its thread and it has to fight for leftover CPU on a core that is already heavily used or something similar to that.
I am definitely not computer-savy enough to tell you how to remedy this but hopefully someone with better knowledge will be able to.
2ms of script wouldn't be noticable on its own, but 2ms of script that was never intended to run this often is not optimized, and is going to generate tons of temporary objects, and garbage collections. Those are the stuttering.
The solution is probably going to be to reload an older point in the save before the script went nuts. The save file would probably help the developers though.