There are a handful of issues that can contribute to 'less than perfectly smooth' footage. Our goal is to make sure you get the best quality footage possible out of your system so here's some potential sources and solutions to the dreaded 'jumpy-choppyness' syndrome:
Couple of reasons this can happen, but probably the most common is not allowing the camera's buffer to clear before taking the next frame or shooting at an interval cycle that's faster than the camera can handle. To avoid this make sure your camera's buffer light is off before the next shot, what can happen is eventually the buffer will overload and the camera will block the trigger signal until the buffer clears enough room for the next shot.
Another potential source is using 'Live-View' or 'Auto-review', typically the camera will block a trigger signal if the camera is displaying an auto-review frame (live view tends to do this automatically). To avoid this make sure you have some focus time set on the controller (a short 0.3-0.6 of a second will do) to clear the auto-review and prepare the camera ready for another trigger signal.
Of course, if the camera's Auto-focus is enabled, this can also cause missed shots. Make sure your Auto-focus is disabled, what happens in this case is if the camera can't confirm focus it will block the trigger signal. It's rare but sometimes a bad cable or a cable that's not totally seated properly can cause missed shots or another rare case is where the trigger time on the controller is not quite enough for the camera to register it but close enough that it triggers sometimes, in most cameras will trigger just fine with 100 milliseconds of trigger time but occasionally camera bodies need up-to 250ms to consistently trigger.
This is an awesome feature for still photography but for timelapse you want to make sure you disable all image stabilization settings. What can happen is the image stabilization will literally move the lens optics or the cameras sensor ever so slightly every time it's triggered. This is a very bad thing for timelapse, you want the camera system to be as locked into place as possible throughout the shot sequence. The irony here is having IS engaged while shooting a timelapse can have exactly the opposite effect.. creating a 'jittery' or 'unstable' look, it can at it's worse look like the system is bouncing all over the place!
This can happen when you have an image sequence or video clip that's being interpreted as 30 frames per second and you then drop that sequence into a 24 frame per second timeline causing a drop-frame situation. Literally every 5th frame will be gone causing a consistent jump.. Here's a tutorial that will help you to understand the correct way to set frame-rates up in Adobe After Effects (it's a very similar process in Premiere). Basically, make sure that your using the same frame-rate for imported image sequences or video clips as you are for the composition. It is not very easy to notice this issue in a static timelapse but it's very apparent in a motion timelapse.. So sometimes we find that shooters have long established bad habits that they were not aware of until they first begin shooting timelapse with motion.
Motion settings are too fast or there are too few frames for said move
This is an issue where some experience over time will lead to better decisions or by simply playing it safe and shooting more frames than necessary.. When your motion is relitively extreme over a short shot period of time two things can happen; the viewers graphics card cannot keep up with the aggressive move (this is particularly bad & ugly with streaming internet video content) or the distance moved per shot is just simply too aggressive to maintain smooth motion continuity.
One solution with with the MX3 is the built in the 'EZ Mode' which takes the focal length into consideration and sets a speed or distance per shot at a conservative rate to produce smooth motion.. Learn more here!