Hi Johnny
using the certification completion editor and viewing the completion record of the user may give more insight into why the recertification window isn't is isn't being opened.
One of the courses may bot be being reset correctly - this could be because it is also in another certification, the course completion condition isn't able to be reset for example using completion of another course won't reset the other course, there is a custom activity that isn't able to be reset or completed correctly.
Regards