Y, not Z, very very important.

src/main/java/com/gmail/nossr50/util/blockmeta/chunkmeta/PrimitiveChunkStore.java

@@ -12,7 +12,6 @@ import com.gmail.nossr50.util.blockmeta.ChunkletStore;
 public class PrimitiveChunkStore implements ChunkStore {
     private static final long serialVersionUID = -1L;
     transient private boolean dirty = false;
-    transient private int maxZ;
     /** X, Z, Y */
     public boolean[][][] store;
     private static final int CURRENT_VERSION = 7;
@@ -25,7 +24,6 @@ public class PrimitiveChunkStore implements ChunkStore {
         this.cx = cx;
         this.cz = cz;
         this.worldUid = world.getUID();
-        this.maxZ = world.getMaxHeight() - 1;
         this.store = new boolean[16][16][world.getMaxHeight()];
     }
 
@@ -56,7 +54,7 @@ public class PrimitiveChunkStore implements ChunkStore {
 
     @Override
     public void setTrue(int x, int y, int z) {
-        if (z > maxZ || z < 0)
+        if (y >= store.length || y < 0)
             return;
         store[x][z][y] = true;
         dirty = true;
@@ -64,7 +62,7 @@ public class PrimitiveChunkStore implements ChunkStore {
 
     @Override
     public void setFalse(int x, int y, int z) {
-        if (z > maxZ || z < 0)
+        if (y >= store.length || y < 0)
             return;
         store[x][z][y] = false;
         dirty = true;