You are miscalculating, or neglecting to calculate, the effect on the capacity of the entire pack of connecting cells in parallel:
- 1S 4P: 3 V
- 3V 3.2A-h 1C charge = 3.2A. Split evenly over four cells, 3.2A = 0.8A/cell
- 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
- 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).