You are talking about two unrelated topics here: note duration and retriggering from the Zendrum.
You mentioned a "heavy-handed" style; my guess is that you are getting some false triggering on your harder hits. Some pads will be more susceptible to this than others, due to their very slightly variable sensitivity, placement in relation to other pads, how rigidly they are attached, how tightly the cap is on, Voodoo curses, and other strange phenomena. If this continues, don't play so hard (from experience, I will tell you that the quieter you play normally, the more dynamic range you have access to), and raise the noise floor setting (FL) in your Zendrum...maybe in the 6-8 range to start with.
Now, as I am sure you know, the Zendrum, sus polarity notwithstanding, has no control over note duration...it sends a Note On message followed immediately by a Note Off. For your "random" mutes, my guess is that something is up in Garage Band...NOT your Zendrum...the Zendrum just doesn't have any ability to create what you describe. Unless, somehow you might be inadvertently tapping the sustain button (because, since you have the polarity set backwards, the sus switch would be like a MUTE switch). Make sense?