Bad path when WordPress has its own directory

At least I’m fairly sure that is the reason why the plugin is exhibiting this behaviour. It was working perfectly fine at first producing the desired path:

wp-content/uploads/permalink

But as soon as I followed the instructions detailed here https://codex.www.ads-software.com/Giving_WordPress_Its_Own_Directory, it began producing paths like this:

wp-content/uploads/http:/domain/permalink

And my template is as simple as that: /%permalink%

Any ideas on how to solve this? The plugin is excellent!

https://www.ads-software.com/extend/plugins/custom-upload-dir/