FWIW I think the problem is that Mail loses track of which window has focus, and consequently does not redraw the insertion bar in the message window.
A workaround is to switch from the active message window to the message viewer, then switch back to the message window.
This workaround works in Mavericks Mail and in Mountain Lion Mail.
To automate the above steps, here is an AppleScript that opens a new message viewer window, switches to it, then closes it, and switches back to the message window. The script hides these actions while they happen.
After copy-pasting this script to Script Editor, you can either save it as a script file in one of the Script Menu's folders in the user account's Library>Scripts folder and access the script from the Script Menu while in Mail, or you can save it as an application and assign a keyboard shortcut to it in Keyboard System Preference.
Hope this helps.
tell application "Mail"
set visible to false
makenewmessage viewer
activatemessage viewer 2
closewindow 1
set visible to true
end tell