Taig mill with Gecko540 driver

I'm at a loss to figure out the configuration I need. The X axis of the mill travels correctly, but the Z and Y axes go in reverse.
I've set up table travel as follows: (inches)
X axis -6 to 6 home at 0
Y axis -2.75 to 2.75 home at 0
Z axis 0 to 6 home at 6

So when I jog the axes pressing minus (-) I get this movement of the tables
X-axis (-) moves the table to right
Y-axis (-) moves the table towards me / away from column of mill
Z-axis (-) moves the spindle up

I actually bought the mill and everything in the US a couple of years ago, and had it set up to test and everything ran fine-- I even have a block of machinable was with the LinuxCNC from the test program carved into it. Unfortunately, I didn't save the config from the computer I was using, which I didn't bring with me to SK. Now I've finally got a workshop space for the mill, and I just can't figure out what I'm doing wrong.

Thanks for the quick reply! I just put a -1 in the pulley gear ration of stepconf for the Y and Z axis (I guess anywhere you can put a negative number on the axis configuration screen (e.g. -200 steps / revolution)), and now it goes the right way. (stepper controlled mill)