Ah, I see - yes i had the same issue and just wound the screw off the stop by hand a few times. Once soft limits are set properly, the issue never occurs again, my soft limits are set 3mm off the hard limits IIRC.
You would think that as Mach knew which way the axis was moving when it hit the limit, it would simply allow movement in the opposite direction, but i Mach is what it is, end of.
What it is, is really a pretty good way of building CNC machinery, there are other options out there now but i have no idea if they are better, the same or worse than Mach3.