It's my understanding that PhD spots are usually far fewer and more fully funded. Logistically, it makes sense to fill those first and then round out the department with the funding and resources allotted for the MA Program, which in some places may only be partially funded or not at all. The delay varies from dept to dept.
So, about the 1 Master's applicant thing: For serious? That would explain a lot, but also sounds shady. Anyway, the letter I received from the dept reflects the same reasons: many applicants and, especially, a lack of funding.