You are miscalculating, or neglecting to calculate, the effect on the capacity of the *entire pack* of connecting cells in parallel:

1. 1S 4P: 3 V
    * 3V 3.2A-h  1C charge = 3.2A.  Split evenly over four cells, 3.2A = 0.8A/cell
1. 2S 2P: 6 V
    * 6V 1.6A-h  1C charge = 1.6A.  Split evenly over two strings of two cells 1.6A = 0.8A/cell
1. 4S 1P: 12 V
    * 12V 0.8A-h  1C charge = 0.8A.  There's just one string, so 0.8A = 0.8A/cell

(As a practical note, you can't trust that a parallel arrangement will split the current evenly -- just be aware).