Not sure if I caught on, am I correct:
1. You're jogging the machine by turning handwheels attached to each axis while the motors are powered off,
2. You want the resulting position to be your starting point.
Which GUI are you using? I experimented in Axis, I can do touch-off and enter a value instead of 0 to tell it where it is starting. You will need to know how far from home you jogged it, and enter that value in touch off for each axis.
EDIT:
Sorry, I was wrong. That will not work. Entering an offset moves the part away from the tool. I think my brain needs sleep soon.
Lacking any other options to reliably jog it, you might use MDI commands to send it to the touchoff point. If it is in incremental mode 'jogging' might be less complicated compared to absolute mode depending how quick you are with math.
Surely switching the jog increments from 'continous' to a specific value would suffice, and be easier than MDI commands. It should then only move the specified distance each time you press a key, if it continues anyway, I would suspect a problem with the keyboard auto-repeat on your system.