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.
Fixing the Issue
If you are not familiar with the .json file format the easiest way to fix
this is to simply make a note of the names in the file and reset it. Once the
file has been reset there should be nothing but two brackets []. When the
file has been reset and the changes have been saved, restart the server. 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.