This issue cannot be reproduced. I have further reasons to believe that the issue is not a bug.
The configuration wizard pops up whenever the hidden configuration setting akeeba.flag.confwiz is not set in the current backup profile or has the default value 0. Whenever you a. dismiss the wizard; or b. run the wizard to successful completion or c. save the profile configuration from the Configuration page this configuration setting is set to 1.
Seeing the configuration wizard pop up all the time means that the configuration is not saved to the database. Try going to the Configuration page and change a setting. Any setting, as long as you remember its previous and its new value. Click on Save & Close. Now go back to Configuration. Is that setting changed?
If it is changed and the configuration wizard prompt is no longer displayed: nothing to do.
If it is changed and the configuration wizard prompt keeps appearing: you seem to have some issue with caching of the generated HTML. This probably means that you have a misconfigured cache, CDN or reverse proxy in front of your server which erroneously caches the backend pages of your site (despite them asking explicitly not to be cached). You'll have to take this to your host.
If it is not changed and the configuration wizard prompt keeps appearing: check that the #__ak_profiles table exists and it has one or more rows. If not, uninstall and reinstall the extension. If the table is there something in your database doesn't let the records save. Are you using a custom database driver for your site or a third party extension which hijacks the database driver?
Nicholas K. Dionysopoulos
Lead Developer and Director
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