We are not aware of any issues with those plugins. I have seen some clients using the iThemes security pro (although I am not familiar with that plugin), and we are using Elementor Pro regularly.
The only case the plugin does not execute the shortcode is, when this option is enabled, and a robot or a very old browser is detected. If that option is turned off, the shortcode is always processed.
On the server administrator panel, check if you have any opCode or Memcached module enabled, if the issue persists when W3TC is enabled, then it might be originated from a higher level cache.