Since this issue isn't present when you create a new user account, I suggest you also test whether this behaviour is replicated in Safe Mode.
Boot into Safe Mode
Follow these steps to boot your MacBook Pro into Safe Mode:
- Fully shut down your Mac
- Restart your Mac
- Immediately press the Shift key and keep it down
- Let go of the Shift key when you see the login window (NOTE: If you have FileVault enabled you may need to log in twice).
- Take a note of what happens (i.e. is the issue still present when accessing System Preferences)
- Now exit Safe Mode by restarting your Mac as normal
- Once logged in again, test to see whether the behaviour continues
If the problem is not present during Safe Mode and still remains when you log back in normally, it's time to investigate login items, fonts, and kernel extensions.
Investigating login items, fonts, and kernel extensions
Let's start with Login Items:
- Startup normally
- Go to System Preferences > Users & Groups
- Select the Login Items tab
- Take a note of your Login Items
- Now remove all of them by highlighting them and clicking on the - button below
- Restart your computer
Now your Mac will boot up without those login items loading. Test this and see if the problem persists:
- If the problem goes away you know one (or more) of the Login items were causing the problem. You can then add them back in one by one until you've identified the culprit. Problem solved.
- If the problem does persist, it's either a problem with fonts you've installed yourself or with a 3rd party kernel extension. A little more info below:
Fonts:- You can remove any of the fonts you've installed yourself to see if this makes a difference.
Kernel Extensions:- You can open Terminal (found within your Utilites folder) and enter the following command:
kextstat | grep -v com.apple
The above command will list 3rd party kernel extensions (you may need to stretch the Terminal window so it's easier to read). Look for anything you don't remember installing, or something that belongs to software you've removed, or just anything that looks out of place. Remember though, this is a list of 3rd party kernel extensions and therefore any of them could be causing the problem.
After making these changes, use your Mac long enough to see what difference, if any, they make. This is basically a troubleshooting step to help narrow down the possible cause of your problem, so let me know how you go.