There is no reason to wait more than a day or two to put the finish coat over a primer. In fact, just the opposite is true. If you wait too long, you will loose the bonding effect the primer has.
What could this "special" primer possibly be? Perhaps the builder has a 1 year warrenty on cracks forming in the new construction, and wants to use the excuse if cracks form that your going to paint anyway?
Steve, what do you think?