I haven't used the GUI version since I'm happy tweaking on the command line, but swappolube adds a file called "tuning" to "/etc/events.d". This directory is where scripts that are triggered by certain events go, and in the case of swappolube the event is starting the hildon-desktop, in other words it is only run when you boot up your N900. Every time you reboot your N900, it boots up with the default settings which is why this file is needed to change the settings to the more optimal values at boot time. Don't worry about it being permanent, this file should be removed when you uninstall swappolube, and you can always check in /etc/events.d to make sure it is. Swappolube should also reset these values back to default when it is uninstalled, but if it doesn't, so long as the file has been removed they will be back to default after a reboot.