Hello Angi, and welcome to Seven Forums.
Using "Run as administrator" would be why the Clean up system files button is not there since Disk Cleanup is running elevated. Run Disk Cleanup normally without "Run as administrator" to have it back since it not running elevated. After you click on the Clean up system files button, it will be gone afterwards as well. Clicking on the Clean up system files button is the same as using "Run as administrator" on Disk Cleanup.
Hope this helps,
Shawn