Temp solution is to use the proper § character instead of &

Using &

Using §

Could you check which encoding the config file is saved with?
(ISO 8859-1, windows-1252, utf-8, etc)

When i use the "proper § character instead of &" my chat just looks like this
http://imgur.com/a/qd7Lv

here is what i have the config set to

"minecraft": {
  "chat": {
    "enabled": true,
    "message": "[§bDiscord§f]:%USER% §7%MESSAGE%",
    "maxLength": -1,
    "usernameColor": "white",
    "customFormatting": true
  }
}

},

Im not 100% sure what you mean by that, but here is a copy of the config im using (with the bot token and channel id removed)

http://pastebin.com/jSFYwvKE

The Config gets saved as a .json file?? if that is what you mean.