No definitive answer on the driver issue from hobbycnc yet.

So I have replaced the Y axis driver and tested the machine today. The Y axis is now getting power but it is not moving. I unplugged and swapped Z and Y. Still would not work on that drive (Y worked while Z did not). I know the motor is good (works when swapped). The board has a brand new drive in it. It holds power when I try to move it which leads me to think that it is not a board issue but a program issue.
I switched the dir and step pin numbers and still no luck. I am running out of ideas of what to try to get the Y axis to respond to mach3. Again, motor is on, can't spin screw (has power) try to jog and no response on machine. I unplugged everything and reseated parallel port and all motor wiring, no luck. Is there anything within mach3 that will basically ignore a drive? All have green check in ports and pins.

I don't know if this has been mentioned before but you may want to try checking Sherline 1/2 Pulse mode (Config / Ports & Pins) then restarting Mach3 and see if this makes any difference.

Tweakie.

I don't know if this has been mentioned before but you may want to try checking Sherline 1/2 Pulse mode (Config / Ports & Pins) then restarting Mach3 and see if this makes any difference.

Tweakie,
No luck on checking the Sherline 1/2 pulse mode.

I am not getting any movement in the Y axis still. After looking over the wiring and double checking the connections, I am getting full connection everywhere. I am not getting any movement though? The motor stays locked but doesnt move. I try and jog, no movement, and the motor remains powered. It shows on mach3 that it is moving but the motor sits not moving at all. It worked flawlessly in past and I have not changed anything so the Dir and step configuration is the same. I have been down for quite some time trying to figure out this one axis and I am running out of ideas to try. Any help would be greatly appreciated.

I have an older HobbyCNc board that I have been using for a number of years, and I believe that most of the problems associated with them by other users over the years have been due to bad solder joints.   Have you reflowed all solder joints for the Y axis as often recommended on the HobbyCNC group?  The other failure issue often encountered is connecting and disconnecting stepper wiring WITHOUT making sure the power to the board is fully discharged.  These may not be your problem, but from your thread, they are a high possibility.

John Champlain