I have the same issue on my machine, but it doesn't seem to cause any problems, actually. As long as you make a new one and it works...
But you don't have to start the license server manually every time, just let it run, i.e. don't stop it, just close the license admin dialog; the license server will keep running, and will start automatically every time you reboot Windows.
Regarding the second question, this "wait" time is not really what you think. It's the time, after a client application loses connection to the license server, after which the license is considered returned to the server (even if the application is still running). Otherwise, if you check out a license, and the application crashes without returning it, it would be lost forever. Now it's only "lost" for at most 120 seconds.
(And no, in case anyone wonders, this can not be used to cheat, to get more licenses
ATK stops working itself, if it loses connection to the license server, after the same time.)