I am having the same issue (and I cannot understand what the last person posted - "plain test" or "plain text"? How do I do that?).
Anyway, I tried using a custom archive slug in the "Advanced" Meta Box menu for the custom post type and it made NO difference. My custom post type is named "mjb-post" and the slug I put in is "mjb". Rather than trying to find my post under "mydomain.com/mjb/my-title", the system still wanted to list the URL to the article as "mydomain.com/mjb-post/my-title". In either case, I could never bring up the article as a published article. (I could preview it fine.) Also, if I found it by searching, a nice excerpt was listed in the search results but when I clicked the title, I was taken to the "Not Found" page. If I tried typing directly in the URL, "mydomain.com/my-title", the system redirected it to "mydomain.com/mjb-post/my-title" and again the result was the "Not Found" page.
Another bit of trivia: When I found the excerpt by searching, I could click the "Edit" link below it (logged in as administrator) and I was correctly taken to the edit page for that post. So the system understands everything about the post except the pretty URL.
I tried disabling EVERY plugin except Meta Box and Meta Box AIO. No change.
I don't know if it makes a difference, but WordPress is installed in a subdomain. I tried switching the .htaccess file for one I used originally to run WordPress out of the subfolder. No difference. The newest version has no reference to the subdomain while the old, original version did, so I'm not sure why the new one works. If I remove the .htaccess file completely, the only page URL that works is the home page, which correctly shows the excerpts but when I click on any title link, I get not only a "Not Found" error, but also that error does not display on the WordPress "Not Found" page because WordPress cannot find the "Not Found" page.
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