The title is a bit messy so I'll try and break it down.

Steps to reproduce:

1. Generate a full dirt platform Chunk Generator (y=90 is the height used below)
2. Join the game, break a dirt block and replace it with water. 
3. Use a hoe and till soil next to the water
4. Wait.

After a while, dirt blocks will appear above the farmland blocks, and the farmlands will remain dry.

To use the attached tester, set the generator in bukkit.yml to "BukkitCGTester"

worlds:
  world:
    generator: BukkitCGTester

Tested with no other plugins.

*Marked as major, because if this issue is widespread, most world generation plugins would be affected