I have Bitcoin Core 0.13.1 (64-bit) and I can't get prune to work
If you put startup commands on the command line, you need to add a dash in the beginning (e.g. bitcoind -prune=2000). 

However, when you put them in the bitcoin.conf, I think they have to be put without a dash (e.g. prune=2000). Yet, in the screenshot you show it has a dash. Have you tried putting it in the bitcoin.conf without the dash?