Mainly posting to support the above info. Here's some additional info that might help:
When we need to output with transparency from Moho, we always use PNG Image Sequence. There are technical and practical reasons it's better to output an image sequence over a movie file from pretty much any animation programs, 2D or 3D...I've described these in past posts so I won't list them here. When we do use Moho to output a movie file, it's usually just for a quick test or preview, not the final animation.
When we need a high-quality movie file with or without transparency, we don't use Moho because Moho's movie output capability is pretty limited. IMO, it's better to take the image sequence from Moho and compile it using a program that provides more user control over the movie format and codec settings. In my case, I like to use compositing programs like After Effects, Fusion, or Nuke, or the video editing program Vegas Pro, but almost any compositing or video editing program should be able to do this. Some video conversion utilities may work well too.
If you really
must use Moho to output a movie file with transparency, it's probably best to use PNG image sequence inside a .mov or .avi container.
Because of the high number of frames involved in your project, I still recommend rendering an image sequence first. This way, if Moho crashes, you can pick up the render from where it crashed, or when you need to change only a small section of the animation, you can overwrite only that section and not have to re-render the entire thing. Then, when you have all your frames ready, load the image sequence into a
new Moho project and export a movie file from this project. (Ok, I guess I just listed a couple of reasons anyway.)
Good luck with your animation!