Stutters

Nope, and Chrome explicitly blocks Flash from running by default, so it's not running unless you're getting and approving a prompt to run Flash, which you aren't... and no, simply having Flash installed doesn't break other stuff.  It doesn't work like that.

If you haven't already, "when in doubt, reboot" is fantastic advice.

If the issue persists, it's much more likely that you're running into a performance or driver issue.  You could try disabling hardware acceleration in Chrome itself to see if that improves or changes things.  If the symptoms go away and Chrome isn't using hardware acceleration, that's a good indication that there's a driver problem.  If it doesn't help, then it's probably something else, but nothing is jumping out at me.

YouTube doesn't use Flash.

YouTube doesn't use Flash.

Please try the following:

• Ensure your video drivers are up-to-date.
• Try disabling hardware acceleration
  • In Flash: How do I disable or enable hardware acceleration?
  • In Chrome: Go to chrome://settings/system, toggle the Use hardware acceleration when available setting

If none of the above work, provide a direct link to the Flash content that reproduces the issue.