I can't at this stage say what iTunes may have done to overwrite any drivers or system siftware - shouldn't have done anything bad. Certainly hasn't on any of my systems.
ANyway, stuttering in my experience is cause by any of these three usual suspects in no order of likelihood:
1/
Something's hogging the CPU. Let us know what Task Manager/Processes reports as having the three highest CPU utilisations whilst stuttering.
2/
Anti-virus scan is occurring. In that case the problem will disappear when the scan is finished.
3/
Graphics drivers have been replaced - but you reinstalled all that stuff.
So what about item #1? And what is your system configuration?
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Posting Virtuoso
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since Aug 2007