Sadly this is a known bug. One of the following options should fix the issue.

  • Delete your config directory, which can be found here: 
    • on Windows: C:\Users\<username>\AppData\Roaming\.maltego\v<maltego_version>\config
    • on Linux: ~/.maltego/config
    • on Mac: /Users/< user >/Library/Application Support/maltego/v<maltego_version>/config
    • Please Note: this will reset your Maltego to factory settings.
  • Run this applescript: http://www.leonamarant.com/2008/04/02/how-to-get-off-screen-windows-back-on-your-mac-os-x-v105/.
  • Instead of deleting the config you can modify the file config\Windows2Local\WindowManager.wswmgr to co-ordinates that are below the top bar.