Sounds like a bug in the PMDX plugin. Be sure to report this to them.
and
You shouldn't have to turn off the softlimits to probe, I don't think.
I can't rule anything out at this point, and it *may* be an issue with our plug-in, but at first glance I would be surprised. Soft limits are handled entirely by the Mach4 core and motion planner. Our plug-in has nothing to do with them. Probing motion comes to the plug-in through the Mach4 motion planner, same as GCode motion. Well, up until the point where the probe makes contact - then the SmartBOB takes over the motion and halts movement (decelerates to a stop).
Since the purpose of this sequence is to set a new zero point for the Z axis, what *may* be happening is that changing the Z position in the DRO and then moving for the probe motion might be exceeding the soft limits. Your profile that I have here has the Z axis soft limits as -7.5 to 0 (presuming that you have fixed the max/min values in the proper, non-intuitive columns). If the canned probing routines try to move the Z axis up (which I presume is toward a more positive position) it may trigger the soft limit when it moves above the zero that you just set. This is pure speculation on my part as I haven't tested any of this.
If you want, enable our debug log to a file, run the tool zero sequence with soft limits enabled, then send us the log file (or the Mach4 package if that is easier). That should tell me pretty quickly if the issue is in our plug-in.