Indeed, export to miniMAD transcodes the videos so it play smoothly on the miniMAD, but it may get a bit of tweaking in the next update.
Changing the source file encoding shouldn't make any difference.
Could you send me the project and movie file in a PM?
You can always try to make trancoding tests yourself and copy the file to /mapping in the MINIMAD partition of the SD-card, in place of the one exported by MadMapper. miniMAD-compatible format is H264 / 420p with .mov extension.
Let us know!