What's the 5V feed to the stepper driver? - sorry, don't understand that. I'm assuming that you're using the BoB to switch the "-" inputs to the driver with a common 5V supply to the "+" - in which case, so long as the 5V supply has a common earth with the BoB it'll be fine.

Faster in one direction than another?, strange - step/dir means that the step generation is independent from the direction signal.

Random thoughts - what's the frequency of the thread that your parport is driven by? (I'm doubting that Linuxcnc will stretch any performance requirements of the driver). here's a thought - slave the step input to your A-Axis to another known axis and confirm the behaviour (different rates/direction) - that'd tell us there's something amiss with the driver.