Very mysterious dropping steps on one Y axis motor...I'm starting to lose it!!

[JAZZCNC]

This is the board I have.
Is the frequency the Kernal speed in ports and pins configuration?...if so it's 25,000hz

Ok so you are using the parallel port now I'm not saying that is your problem, thou it's highly possible, but what I am suggesting is you do yourself a favor and buy an external motion controller like the AXBB-E which uses an Ethernet connection. Combine this with more volts for the steppers and you'll transform the machine into a different animal.

It will be more reliable and faster, you'll also be able to dump Mach3 and go with UCCNC software which is much better.

Now back to your issue.!

Because you are using the parallel port some of this could be because you have the machine overturned, So give us the settings you have for the motor tuning and the micro-steps set on the drives for each axis.

Also, have you checked the STEPS PER is correct by measuring it moves the correct distance told.?