No, I have not had a single report of the probing not stopping the tool. I would guess that it's an electrical issue?
can you try using 3.42.040? If it does the same thing with that version, then I'd say for sure it's an electrical issue.
I have had two users report random, strange issues with the newest release.
One was the probing wizard would crash if opened more than once. Using 3.42.040 fixed this.
The other user reports that the macro seems to get lost during tool changes, if too much time passes while it's waiting.
Unless you need something in the latest versions, I really recommend using 3.42.040, as it just seems to be more stable. (I'm sure some will disagree.)
As for the probe length. You'll need to modify the M6End and M881 macros. Near the top of each, there is a section that defines the travel and feedrate for both inches and mm's. It should be easy to spot and change. Let me know if you need more help.