Here is it works.

The seed, or lack of seed, is determined at the moment of planting. So if you plant the corners first and then the sides the corners will never set seeds. You MUST plant the seeds next to another seed. See the diagram on this page: http://www.ffxivgardening.com/planner.php

This also means that the first seed you plant will never set seeds. If my planting includes something like karkka or curiel roots I will plant the first seed with grade 3 shroud topsoil. If its something like a minion or an essentially valueless crop like mandrake I will plant the first seed with the cheapest grade 1 soil I can find.