To verify if you are connecting to your own Aligner License Server, please do the following:
1.) Open the Aligner License Server so that you can see the current users
2.) Start CodonCode Aligner
3.) Wait until you see the dialog that tells you that your license key is invalid and leave this dialog open - do not click on either of the buttons and do not close it.
4.) Look at the Usage of the Aligner License Server. If you do not see that your license is in use and that you are the current user, you are not using your own license server.
If you are not using your own license server, please change the "License Server" settings in CodonCode Aligner to connect to the correct License Server.