If you run AkelPad's built-in updater (AkelUpdater.exe) e.g. to update plugins or scripts (you can also update AkelPad itself this way), by default the updater wants to relaunch AkelPad, however AkelPadPortable.exe does not wait for AkelUpdater, and thus it moves AkelPad's settings back to the
Data directory when you close AkelPad (which AkelUpdater asks you to do), causing the app to break the app out of portable mode when AkelUpdater relaunches it.
Adding WaitForExe1=AkelUpdater.exe fixes this.
Pull Request # 1 [Merged].