Brian,
Not surprised, assume a lot of people haven't tried the latest version yet, like me, as i am using 3.042.12.
SS is Super Stepper which provides for using the USB port, forget about it.
I couldn't find anything about Mach not saving the step & direction value other than around Ver 2.61.
Sorry, but for such a PITA, you think i would have remembered what fixed it or what i did.
That said, maybe someone else may post about it.
RICH