I assume you mean you get the single line with no notes after rendering, yes? Remember that rendering isn't just rendering Melodyne, but any other clip attributes. So what you experience will happen if a clip is muted, whether on purpose or buried in a Take Lane. Rather than chasing down what the issue is, you can just ctrl+drag the clip to a new track, apply Melodyne, then move it back to the original track.
Also make sure you download the latest update to Melodyne 4, one was issued shortly after it appeared.