I'm using the same setup and getting the same behavior. I guess that means your experience isn't an anomoly.
I've mitigated the issue by using velocity jogging mode only in the x100 setting (for coarse positioning). In the x1 and x10 settings, I'm using position jogging mode for exact control, and the overrunning behavior goes away.
With this configuration, I've never had the overrunning behavior cause a crash, and in fact, I've even taken advantage of it for making long, steady moves without the need for programming. Admittedly, it does require a little technique, but it's quicker than typing a G1 move.
For what it's worth, I used keyboard jogging controls for 5 or 6 years, and now that I have the pendant, I could never live without it.
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