Yeah, the planner is not perfect. You'll get slightly different numbers on different parts of the trail or at different speeds/day lengths. The algorithm behind the planner does a pretty complex simulation where it has to balance a few different goals (e.g. resupply needs and days that aren't excessively long). It tries to schedule the zero days for places where there's a hotel/hostel. If there's a long distance between beds (e.g. Maine), it doesn't do an awesome job of placing a zero day at the interval that you give it.

Thanks for being interesting in how the wikitrail planner works! It tries hard to make people happy. Feel free to add in additional zeros.