This sounds more like a hardware issue.
I'd contact NI tech support and tell them about it!
BTW, I'm currently working on a Ableton Live set that makes it easy to play chords & inversions of one scale on the Maschine. What it basically does (please correct me if I say something wrong, I actually have little to no idea about music theory):
1. You hit a pad in the keyboard mode of Maschine group G, sound 1 (that's what I use at least)
2. MIDI notes gets sent from Maschine standalone to Ableton Live standalone via MIDI (using virtual midi cables like LoopBe / MIDIYoke, the built-in Mac OS X feature for that or a plain old MIDI cable)
3. Ableton Live translates each pad note into a chord
4. Chord is sent to Maschine group C, sound 1 (that's what I use)
5. Chord is heard in Maschine. No need to exit the Maschine standalone!
This happens nearly instantly (there is a tiny delay of a few ms, but quantizing by 50 % just once will fix that).
The pads are laid out that every uneven pad (e.g. 1, 3, 5, ...) plays a 'normal' chord (like C, D#, G), while every even pad (e.g. 2, 4, 6, ...) plays an inversion that is within the pitch of the sourrouning pads. You can select which inversions you want on the even pads in the Ableton Live set or by turning a knob in the custom Maschine controller template.
As of now, I only have chords mapped out with 5 notes (I think they are called ninths? Like C, D#, G, A#, D) and the matching 4 different inversions on each even pad, as I'm really into these jazzy Deep House chords. I may add triads and sevenths if someone could use that.
It's really easy to jam around and try out chord progressions, even if you know shit about music theory