thats a pretty fine tolerance your trying to work to!
i have a 321 .
that size hole would be way out of tolerance without slowing it right down. and i would probably choose a 3mm bit if i wanted it near accurate.
your new machine code is probably made of lots of small segment moves ? or the machine is trying to keep within the encoder counts. your asking for less than half a milimetre movement in circular interpolation, thats pretty hard to achieve for a big gantry machine
have you thought about using a drill for those holes???