Hi Jackie.
The assignments tab determines how long users are given to complete the certification. The minimum time allowance in the course set is only used to make sure that users are not asked to complete the certification is less time than is required for the course sets to be completed. "Set realistic time allowance" also uses this to calculate how much extra time to grant users when resolving exceptions, so by saying the course set takes 0 time, you're saying that they don't need to be given any extra time to complete it, so I think in that situation it will give them a default of 1 week.
The "Complete by" in the assignments and the due date in a user's certification are two different values. One problem you might experience is that changing an assignment "Complete by" doesn't cause the user's due date to be updated if a user's due date has already been calculated. This is because a user's due date may have been modified by being given an extension, resolving exceptions, or by the recertification process, and the system has no way of knowing if one of those events has occurred. Even if it did know what had happened, it couldn't make the decision as to what action is correct in each situation, so instead it makes no changes.
For everything to work correctly, set a reasonable minimum time required for the course sets and either set no "Complete by" in the assignments, or else set a "Complete by" which is at least as much as the minimum time required to complete initial certification. You should also set your recertification window to be at least as long as the minimum time required to achieve recertification.
Nathan