Be sure you don't have the files set to "Read-only" and that you are editing the correct file in the correct place (Documents\The Witcher 3\user.settings). It could also be a result of the file being synced with some form of cloud storage that is automatically restoring a synced user.settings. Either way, the game will only rebuild the file if it is missing or you're installing, patching, or verifying/validating.
Until the cause of the issue is known, that's impossible to answer for certain. It certainly does seem to be something related to hardware/drivers, as most users do not experience this. Best bet is to send the issue into CDPR Support directly.
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Additionally, if users on this thread could post their GPU, Driver Version, and Windows Version, it could help to start narrowing down possible sources of the problem.
Ok so I did a fresh install and had no mods running - went up to a Venomous Arachas and the stutter occurred. I will look for rot fiends and sirens to confirm - but this at least eliminates the mods and sweet fx.