I am having a similar issue.
I am able to get /%custom-post-type-name%/%custom-post-category%/%postname% to work for my project pages but when I set the category base it breaks the project page. So I am trying to obtain consistent URLs like:
– mydomain.com/projects/category-name/
(This requires the category base rewrite to add “projects” before the category name. This will work but breaks the project page below and vice versa.)
– mydomain.com/projects/category-name/project-name
Hope this is clear enough to follow. Any help is greatly appreciated.