What does your Gcode look like

If the moves are so short that MAch3 cannot get up to speed in that distance then you are limited to the time base of the moves.
IF you can drill at wide open speed then a straight gcode program(no canned cycles) drilling with G00 will be the fastest possible means.
Post a copy of your gcode and I will take a look at it.
One way to look at it is take all the distances of all the moves and divide by the time you will then get the average DISTANCE/time that the machine is doing.
Just a thought, (;-) TP