How long are you waiting before for quitting Aperture? Aperture needs to upgrade the library, and that can take a long time. Let it run.
Also, the first few times after the upgrade it will take longer before you can access the menus.
Several users reported that they had to wait at least 40 seconds after each launch, after the initial library upgrade completed. And that background processing will be done, slowing Aperture down.
Let Aperture get the background processing done without interrupting it.
From Aperture's Release notes: Aperture 3.6 Release notes
Keep in mind that fully upgrading a very large library is a one-time process that can take a long time; the process may take many hours or even overnight, depending on the size of the library. Once the initial database upgrade is complete, you can begin working with your Aperture library. However, post-upgrade processing will continue in the background for some time, as face detection and preview generation are performed. (A progress indicator and the word "Processing" will appear in the status line of the Viewer or Browser to indicate these operations are underway.) While you can work with Aperture while these operations are performed, you may experience temporary slow-downs. Optimal performance will return when all post-upgrade processing is complete.