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If the problem is still there, try booting into the Safe Mode using your normal account. Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer or by using the developer’s uninstall instructions. For each disable/delete, you will need to restart if you don't do them all at once. Please post if this worked or not.

Safe Mode - About El Capitan
also Sierra

Safe Mode Startup – El Capitan. also Sierra

If it works in the Safe Mode, try running this program when booted normally and then copy and paste the output in a reply. The program was created by Etresoft, a frequent contributor. Please use copy and paste as screen shots can be hard to read. Click “Share Report” button in the toolbar, select “Copy to Clipboard” and then paste into a reply. This will show what is running on your computer. No personal information is shown. You can run the report for free at least once, but if you run it several times, at some point it will ask you to pay a license fee.

Etrecheck – System Information