Since live playback is just fine it cannot be due to system inadequacy in any way. It must be something that only happens during MIDI render, which implies a software problem.

It sounds like some wacked "humanize" effect. As if humanize is set to "maximum annoying" during a render.
Also, render is dropping notes again, so it isn't a 1-off. That seems to be the bigger problem. At first the notes are all there, but about 1-minute into the song they start disappearing until they are all gone.