In order to automatically create 301 redirects, you need to use the Update URLs function. Just change the configuration, then open JoomSEF's URLs Manager, select URLs that you want to update, choose the Update URLs action in the second select-box in toolbar and click the Proceed button. Selected SEF URLs will be updated and if they change, the 301 redirect will be created from old URL to new one. You can check this using Manage 301 Redirects page.
I'd suggest updating only one SEF URL first, to check if everything works correctly. If it updates and 301 redirect is created, then you can update all the remaining URLs at once.