That should have just been the beta license timing out. We do not (necessarily) uninstall the license file when you uninstall SlickEdit. When a license file is installed using the License Manager, it is copied down into the Application Data folder on Windows (not sure where we copy it on Linux...), which is where we look the next time SlickEdit is installed. Uninstalling SlickEdit won't remove the license from that location.
SlickEdit will also look for a license file in the win/bin directory. If you copy the license file there, it will not need to be installed using the License Manager. That file will be uninstalled as part of the SlickEdit uninstall process. The downside to this approach is that you will have to copy a license file back the win/bin directory each time you upgrade to v14.0.1, v14.0.2, etc.
So, depending on how you apply the license file, a clean install directory does not necessarily mean that the license has been removed.
@dunkers: Though our installer used to request a license, it shouldn't be doing that now. SlickEdit checks for a license each time it is launched and displays the License Manager if one cannot be found. That is the point where you should be prompted for a license, not as part of the installer. It should come up after you click "Finish" on the installer if you have the "Launch SlickEdit..." checkbox checked. Though I'm hesitant to suggest it, I'm hoping you are misremembering the sequence of events.
Now that the perpetual license has been installed, you shouldn't see any further warnings about SlickEdit 2009 not finding a license. Of course, when you upgrade to SlickEdit 2010 you will need a new license.