The fact that all three axes are loosing steps is suspicious but the feed rates do seem high so that might explain it - are you running ball screws. Where did the configuration parameters come from?

I use EMC2 and don't know much about Mach 3 but a quick skim of the manual found a couple of references to step pulse width and inversion...

"Pulse width is another consideration. Most drives will work well with a 1 microsecond minimum pulse
width. If you have problems with the test moves (e.g. motor seems too noisy), first check that your step
pulses are not inverted (by Low active being set incorrectly for Step on the Ports and Pins>Motor
Outputs tab), then you might try increasing the pulse width to, say, 5 microseconds. The Step and
Direction interface is very simple but, because it can still “sort of work” when configured badly, it can
be difficult to fault-find without being very systematic and/or looking at the pulses with an oscillo-
scope."

So if the motors sound rough at moderate feed rates it might be worth checking that the low active or high active setting is set to match your drivers. What machine is it you've got? Are there any technical documents with it?

As Mark says, it's all part of the learning experience - I've got a couple of parts on the mill that need remaking due to it loosing steps while I was making the parts needed to stop it loosing steps :-)