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.
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.