The cause of the star trees' poor growth seems to lie in the Toraimarai Canal. First, bring some silk cloth to Profressor Koru-Moru so he can improve his magic doll. Then take the magic doll into the Toraimarai Canal to carry out an inspection.
The quickest way to finish this cutscene, is to use the Toraimarai Canal Survival Guide teleport. It places you right outside of the zone to the ruins. This is right by the Gate of Earth.
Examine the Gate of Earth at (I-7) for a cutscene.