In light of your findings, you may want to consider a SS instead of the graphics card. The SS may well cure your problem too and it looks like it will have a much longer life expectancy then the parallel port. The parallel port is dieing and having a SS may allow to upgrade easier in the future. I can't guarantee any of this but I think I would consider it.
Here is a quote from an email I was copied on concerning soft limits and it sums them up is as a few words as I have seen.
Soft Limits are described in section 5.6.1.3 of the "Mach3Mill Install and Config Guide"
If you were trying to setup Soft Limits, then make sure that you have a consistent Homing strategy (since Soft Limits are based on Machine Coordinates) and double-check that your min/max values are correct - the easiest way is to home your machine, move each axis to it's furthest extent, and see what the values are (by click on the Machine Coords button on the Program Run screen). Those values, along with 0, make up your min/max (ie. if X is 0 at one end of travel, and -43 at the other end, then your Max will be 0 and your Min will be -43; if Y is 0 at one end and +20 at the other, then your Max will be +20 and your Min will be 0)...
Brett