The probable cause is that your power supply has not had time to completly discharge between each power cycle. Then as the power is turned back on the residual voltge creates a "pop".
SOLUTION: Decrease the value or add a bleeder resistor on your system power supply input. Of course, part of the system power supply will drive the bleeder resistor unless you add a switch (MOSFET) to disable it.
The best solution is to not cycle the power rapidly, but if your system specification requires rapid power cycling, the above should help.