Yes, SimToolkitPro and all included tools (and some future ones) are and will continue to be provided for free. There are plans for 2 complex modules that will be developed once SimToolkitPro matures some and these will be available for one-time purchase and will be very reasonably priced.
Find and remove the SimToolkitPro in your roaming AppData folder. The quickest way to find this is use the windows key + r to open the run dialog, enter %appdata% and press enter. Find and delete the entire SimToolkitPro folder and start the app again. This will reset your settings, but will retain all of your reports.
This is an ongoing issues. Usually resolved by restarting SimToolkitPro with X-Plane already running. A fix will be shipped as soon as it is available.