I have noticed when opening sql files that the sql editor puts in connection bar at the top. All very logical of course. Unfortunately this bar cuts of the top part of first line of the query, which is annoying if nothing else. Obviously, adding an empty line helps.
I run MyEclipse on a Debian Lenny platform. MyEclipse was installed via Ganymede as an update site. Additional plugins are subversive and a custom plugin.