Since TYPO3 the option 'Flush system caches' isn´t needed anymore because of the new option 'Flush all caches', which clears all system-related caches.
To activate the "Flush system caches" option in the TYPO3 backend, you need to add the following code into your User TSconfig.
- Navigate to System > Backend users > [your username] > Edit > Options in the TYPO3 backend.
- Add options.clearCache.system = 1 into the field TSconfig.
- Click on save and reload your backend (or log in with the account you made the changes for) and you should see a new option "Flush system caches" below "Flush general caches".