I have only had corrupted downloads do such things. When eMule is completing the file, it checks if all chunks are OK. If they are corrupted, it throws those parts out and remains unfinished. You will have to re-download those parts.
However, what you describe sounds more radical. What happens to the ddownloads? They freeze? Or they get deleted? Or...? What's the difference between the downloads that survive and those who don't? For example: all downloads who survive are good movies, all that don't are p0rn