bakr
you must increase the power of your fly-back circuit for faster charge. for this increase the inductor current before switch off. by doubling this current the pulse energy will rise 4 times than before (square of current rise).
good luck.

 
haw fast is switched off your IGBT transistor?
if is too slow then this is your problem.
or output diode - same question.

 
An fast(non-electrolitic) cap must be in parallel with output electrolitic cap for fast response.

 
no diference in current, we talking about diferences in conduction mechanism.
If carriers are in thermic equilibrum with the cristaline network the main difference (from electical conduction point of view) between electrons and gaps is the mobility of their movement throgh the cristal.