With personal licenses (not including Trial licenses, which only allow a single activation), only one copy of Geneious may be open and running at a time with the license. Geneious will display this message if another copy of Geneious is already running with this license, and will then open in restricted mode. You will need to close both copies of Geneious and reopen one to clear the error.
Note that the running copy of Geneious may be on another computer, on another user account on the same computer, or it may be a different version of Geneious on the same computer.