Circuit to prevent spark from plugging Li-po batteries into motor driver with filtering capacitors
The way you describe it, it sounds like the inrush current caused by your capacitors charging up.

For that you could use a limiter, such as a thermistor, or a soft-start circuit, such as a large pass FET with an RC timing circuit. The latter's RC would turn the FET on slowly enough for the capacitors to charge smoothly but not so slowly that the FET gets hot (500 ms?).

Are you sure that your motor load is off when you plug in, though, and have you got any power-up circuitry to ensure this?