TLDR;
Set VSync On in the game.
Just wanted to give you a report of solving stuttering issue so others might save some time trying to chase that one.
My gameplay on the version 11.15 was butter-smooth. I returned to Factorio after version 12.0 was out. What I noticed was some stutter every few seconds. It was not that problematic but nevertheless annoying. I searched the forum but no one really reported such problem. Version 12 brought much awaited performance improvements but the game ran superbly previously for me as well.
Lately the stuttering was becoming more and more annoying and visible, happening every 10-15 seconds. Over the weekend I decided to try and solve the issue. Tried various versions: 11.22 (the earliest I could get for 11 apart from my saved 11.15), and 12.0 - 12.8. Tried full screen / small window. Tried various graphics memory settings. With mods or without. Loading a save / starting a new game. The behavior stayed the same in all those cases.
Tried even to record the gameplay using Fraps as an evidence for a bug report. However, the playback exhibited very strange behavior. The video itself would stutter randomly or play smoothly when repeated. So I started suspecting the graphics card.
Next I searched the internet. There were a few reports of stuttering but most were associated with bad drivers / DPC latency issues. Since I confirmed it was not a problem with my system, as a last resort I checked the Fraps timings recording. The graphs were very much different between those two v11 versions. I was almost ready to report a bug / technical problem on this one as a change between 11.15 and 11.22. However, I decided to check one thing still - the VSync. I had it off on the newer version. I must have turned it off at some point but didn't spotted the difference.
The problem with Factorio is that it always runs at 60fps, irrespectful whether VSync is on or off. The only visible framerate difference is in the menu. For me, the game always stayed at 60 fps (reported both in Fraps or the game itself). I knew then it wasn't a framerate problem (insufficient performance, tearing, etc.) What it looks like is that without VSync the game everu now and then desyncs itself from the monitor refresh and gets into not really tearing but more of a stutter. After 2, 3 seconds it gets back into the margin of synchronicity and the gameplay is smooth again.
After setting the VSync to on, the gameplay is super smooth again (still at 60fps).
Check the graphs:
VSync ON
VSync OFF
If you want, you can generate the graphs using FRAFS Bench viewer (http://sourceforge.net/projects/frafsbenchview/)Specs
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