All worlds should be saved on save-all. Player data should be saved when a save occurs.

src/main/java/net/minecraft/server/ConsoleCommandHandler.java

@@ -28,7 +28,7 @@ public class ConsoleCommandHandler {
                 this.b.a();
             } else if (s.toLowerCase().startsWith("save-all")) {
                 this.a(s1, "Forcing save..");
-                worldserver.a(true, (IProgressUpdate) null);
+                this.b.f(); // CraftBukkit - We should save all worlds on save-all.
                 this.a(s1, "Save complete.");
             } else if (s.toLowerCase().startsWith("save-off")) {
                 this.a(s1, "Disabling level saving..");

src/main/java/net/minecraft/server/MinecraftServer.java

@@ -198,7 +198,7 @@ public class MinecraftServer implements Runnable, ICommandListener {
         server.loadPlugins(); // CraftBukkit
     }
 
-    private void f() {
+    void f() { //CraftBukkit - private -> default
         a.info("Saving chunks");
 
         // CraftBukkit start
@@ -209,6 +209,8 @@ public class MinecraftServer implements Runnable, ICommandListener {
             WorldEvent event = new WorldEvent( Event.Type.WORLD_SAVED, world.getWorld() );
             server.getPluginManager().callEvent( event );
         }
+
+        this.f.d(); // CraftBukkit - player data should be saved whenever a save happens.
         // CraftBukkit end
     }