I believe there is a bug in the new preference loading mechanism. When the checkbox item Repeat Play on Stop is modified and saved it is not correctly reloaded. Visually, the checkbox items will be checked or unchecked as they should be but the underlying boolean values are not updated. To fix this problem, the resetToPreferences method in the console class should have the following line added. setShouldRepeat(repeatButton.isSelected()); Alternatively the shouldRepeat variable could be eliminated and the value could be determined by checking if the checkbox isSelected method returns true as is done in the case of the Increment Seed on Stop checkbox. In my Console class I have also added a property called "Automatically Stop after Seed." This allows me to run a specified number of trials and then stop. If others would find this functionality useful I can share the code.