Whitelist enabled in the server.properties but not working
This is caused if the whitelist.json file format is broken. Whilst the other .json files will crash the server if their layout is broken, the whitelist file may simply stop functioning on some server versions.
The easiest way to fix this, if you are not familiar with the .json file layout, is to simply make a note of the names in the file and reset it (There should be nothing but two brackets, , in the file when it is reset). When the file has been reset and the changes saved, restart the server to start it up. To add people to these files afterwards use the 'whitelist add [name]' command through the console for each player you wish to grant access to the server (including yourself)