The "Flush system caches" menu entry is disabled when TYPO3_CONTEXT=Production.
You can enable it in the backend user's TSCconfig settings:
options.clearCache.system = 1
Also see http://blog.reelworx.at/detail/typo3-cms-clear-cache-buttons-explained/
1 2 | options.clearCache.pages = 1 options.clearCache.all = 1 |