Before doing anything, close Caffeine down if you have it open, remove your existing version of Caffeine and purge it.
sudo apt-get remove caffeine
sudo apt-get purge caffeine
sudo apt-get autoremove
Then, you need to download this version of Caffeine:
https://launchpad.net/~behda/+archive/ubuntu/ppa/+files/caffeine_2.5.1+546~behda~ubuntu13.10.1_all.deb
Once installed, you need to lock this version so it does not get “upgraded” to the latest (inferior, in my opinion) version whenever you run updates or upgrades.
To do this, copy and paste the following in a terminal:
echo caffeine hold | sudo dpkg --set-selections
At which point, if you re-open Caffeine, you will find it works well like it used to. That is to say, with a panel indicator and the capacity to nominate specific programs to trigger it.
Why, in God’s name, it was ever “upgraded” to the newer, inferior, version is beyond me.