Axis “Y” only goes in one direction after upgrading from 2.7 to 2.7.11

Axis “Y” only goes in one direction after upgrading from 2.7 wheezy to 2.7.11 wheezy
I upgraded to the latest 2.7.11 because I couldn't get the rs485 to control the Huanyang VFD correctly, the upgrade fixed that for the most part.
I now have a new problem with my “Y” axis that is just driving me crazy. It will only move in one direction. I am using a Geckodrive G540 to drive my steppers, here are all of the things I have done to find the cause but am unsuccessful so far....and lost at this point.

1 . Swapped X drive plug with Y drive plug (problem was still on the Y output plug)
2. Took G540 apart and swapped Y axis board for the A axis (problem still follows the Y output position)
3. Put old version linuxcnc folder back in place of new 2.7.11 upgrade folder (problem still persists)
4. Started a new configuration via “stepconf” (problem still persists)
5. When I'm in “stepconf” (problem still persists Y axis moves only one direction no matter which green arrow I push)
6. When I'm in “axis.ngc” the readout shows that the Y axis should be moving back and forth according to both the graphic and the numbers that represent position but Y does not.
7. “axis.ngc” shows that I should be going back and forth in the “DRO” output as well as the hal meter.
8. Checked all homing and limit switches.
There has to be a corrupt file somewhere but I have no idea where to look. Any help would be wonderful as this VFD and spindle instal was my last big hurdle before actually using my cnc.

Bad parallel port? I would check the Y direction pin on the parallel port with a meter
And if that doesn't work (change voltage when jogging back and forth),
I would try to toggle the pin by hand with halcmd

Well this embarrassing After some troubleshooting and discovering a low voltage on pin 3 when using the ptest.hal, I bought a parallel card thinking my port was bad but it wasn't. Shortly after I upgraded to 2.7.11 I had a power supply failure in the computer and apparently while changing the power supply I inadvertently pulled on the ribbon cable that connects my P port to the DB25 connector just enough to unseat a ground or something. So that is fixed and I have an extra Parallel port card now.

Just a quick question on charge pumps. Do I need to add any code to my hal file before applying the 470ohm resistor fix to my parallel port mentioned in post # 99193 21 Sep 2017 03:28 or is that not necessary in 2.7.11 ?

CORRECTION Pin 5 was 2.4VDC and did not change state.