Speeds and feeds deep drilling

[JAZZCNC]

Oh Man-O-Man your massively out of wack with those settings.? . . . 3mm peck and 300mm/min would be easily achieved.
My spindle spins twice the speed and I peck at 5mm and 800mm/min with no problems. I can and do drill straight thru 20mm plate single pass @600mm/min at times if just few holes and I'm in a rush, I often drill 12mm plate in 2 pecks no matter how many holes.!!

By the sounds of it you have other issues thou and those need sorting first.? Obviously go thru all the usual checks for sticking or binding etc.
Really you shouldn't be having missed steps at these feeds even without any counter balance so I'd be suspect of the drives or BOB and connections if there's no mechanical issues.
Check the drives and motor connections etc, make sure you have the motor phases correct on the drives IE: A+ A- not switched round.

It could be you have the control settings screwed up.? What you using for control Mach3 or EMC.?
If Mach then what's the motor tuning settings.?

[JAZZCNC]

Oh forgot to say Check your motor couplings or pulleys are not slipping.? Mark them with paint.