That sounds very odd. The images are stored in a subdirectory of your local calibre configuration directory. Go to preferences -> misc and click the open configuration directory button. This plugin will store the images in a resources/images/generate_cover subfolder from memory.
Please attach your Generate Cover.json file to a post for me to take a look. You will find this in the plugins folder of the same calibre configuration folder above. Also run it in debug mode by using ctrl+shift+r and see if there are any errors being displayed and post that here.