We know comments use minimarkdown, which discards newlines. Thus, the Enter key submits the comment instead.
Flag messages also discard newlines. The Enter key, however, inserts one instead of submitting the flag.
I agree that this might trigger angry flames from the people who hate the comments behaviour suddenly starting to submit partial flag messages (although I only have ever seen one or two flag messages that might've used one.) However, that's how it should work.