There is a way, but I can't get it to work, you can use
@Metadata("MyModID")
public static ModMetadata meta;
And modify that, or you can get the metadata from @PreInit.
Can you post logs, preferably from sessions where you start a new world, and experience the problem again? Ie start a new world, then fly around until you get the glitched chunks?
NBTs are Minecraft's in-game storage format, and you can use a TileEntity (not sure about blocks) to save data directly to them. So you really only need one block, and all the properties can be set via NBT.