I do not use G54 or G55 in my code.
Could the problem lie in my pulses being to fast? Parallel Port?
You do, you use at least G54 as you can not use anything else unless your code has a G53 on every single line of code.
G54 is the default offset and it is the numbers you have in the DROs and it is the offset you are changing when you zero an axis..
Please try doing the Ref all as I mentioned above, it will set your machine coords to zero and then you can move to where you want and zero each axis and that will set your G54 offset to zero and you can start again.
Pulsing too fast is not good and will definitely cause you problems, if you are not running Mach when getting that message then there does indeed seem to be an issue with your computer and the pulsing engine.
Hood