So I went back to an older back up of my server when I first installed the mail program. It had a correctly populated database. So I installed the entire directory back on my server. It works properly with /Mail Box and /Mail Playerlist. If you type /Mail without a second split.command argument (/Mail alone) it does not catch it and gives you that array error. So it is, just an annoyance.
Not sure why the newly installed jar would not build the database. I guess if you find the original public build files, you could add a pre-if catch such as; if (splitCommand.length==1){ which would skip to a return or informative error message if the command line did not contain a second split command argument.
What would be a nice upgrade for the future would be to set up a mail box for each player upon arrival on the server so you could auto send them a welcome mail message. Just a thought. Thanks for doing this as I think it is important for players to communicate with each other even if they are offline.