Hmmm, seems there used to be a setting for this, like Place Reply above/below quoted text, but the only thing I find related is if you're using Signatures, Mail>Preferences>Signatures>Place Signature above quoted text, which can have some strange effects.
Have you tried it composing in Plain Text instead of Rich Text?
I think the problem is likely the source, do those interim Apps allow you to show Invisible characters, I use Tex-Edit Pro to display those Home, Paragraph. GR, LFs, etc.
Heh. Here's an even crazier example:
If I am in Mail.app, and I select text in a message I am composing, cut it, then try to paste it somewhere else in the message -- the text is inserted ABOVE the paragraph in which I'm trying to paste. (just like my example earlier)
If, however, I switch to a text editor (BBEdit), paste my text, reselect it, cut it, then switch to Mail.app to paste it in -- it pastes precisely where I intend.
Why on earth would copied text in a mail message be impossible to paste properly???
I have the same problem. It also happens in notes.
Now I created a note in Mail on my Macbook and had this problem: Backspacing a line moved it above the previous paragraph. Then I opened the same note on my Ipad, and I did not have the problem, I could simply backspace the same line and it was connected to the end of the previous paragraph. What I did see in my Ipad note however was that the two paragraphs had a different font (which was not visible on macbook, until I edited it on my Ipad). Somehow my macbook mail creates unsolicited separate paragraphs, which use different invisble fonts, and these paragraphs may not be merged.
The same problem probably also causes email messages that I compose on my macbook to end up at the recipient in a very different font (i.e., lines/ paragraphs are larger and/or in different font.) than what I see when composing the message. This is really annoying, because it makes you look like a complete moron who is unable to compose a properly edited message.