I'm playing Minecraft version 1.3.2, using a profile to place save files in a dedicated directory.

The worlds created in this version are placed in the correct directory (of my choosing), but the save files are read from the .minecraft folder. New worlds are thus 'disappearing' from the worlds list in game (they are saved to a different directory than they are read from).

When opening a world placed manually in the .minecraft save directory, the changes made are persistent (which is strange to me).