Got all the startup issues with motherboard resolved, which were apparently the reason that the joysticks were not initalizing on startup correctly.

src/main/java/jace/apple2e/Apple2e.java

@@ -124,7 +124,8 @@ public class Apple2e extends Computer {
         if (motherboard != null && motherboard.isRunning()) {
             motherboard.suspend();
         }
-        motherboard = new Motherboard(this);
+        motherboard = new Motherboard(this, motherboard);
+        reconfigure();
         motherboard.reconfigure();
     }
 
@@ -132,7 +133,6 @@ public class Apple2e extends Computer {
     public void coldStart() {
         pause();
         reinitMotherboard();
-        //getMemory().dump();
         for (SoftSwitches s : SoftSwitches.values()) {
             s.getSwitch().reset();
         }
@@ -143,10 +143,6 @@ public class Apple2e extends Computer {
         }
         reboot();
         resume();
-        /*
-         getCpu().resume();
-         getVideo().resume();
-         */
     }
 
     public void reboot() {
@@ -477,4 +473,8 @@ public class Apple2e extends Computer {
     public String getShortName() {
         return "computer";
     }
+
+    private void attachMiscDevices() {
+        throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+    }
 }

src/main/java/jace/core/Device.java

@@ -110,6 +110,7 @@ public abstract class Device implements Reconfigurable {
 
     public void resume() {
         setRun(true);
+        waitCycles = 0;
     }
 
     public abstract void attach();

src/main/java/jace/core/Motherboard.java

@@ -58,9 +58,14 @@ public class Motherboard extends TimedDevice {
     /**
      * Creates a new instance of Motherboard
      * @param computer
+     * @param oldMotherboard
      */
-    public Motherboard(Computer computer) {
+    public Motherboard(Computer computer, Motherboard oldMotherboard) {
         super(computer);
+        if (oldMotherboard != null) {
+            miscDevices.addAll(oldMotherboard.miscDevices);
+            speaker = oldMotherboard.speaker;
+        }
     }
 
     @Override

src/main/java/jace/hardware/Joystick.java

@@ -197,13 +197,13 @@ public class Joystick extends Device {
 
         @Override
         protected void doEvent(RAMEvent e) {
-            setRun(true);
             readJoystick();
             xSwitch.setState(true);
             x = 10 + joyX * 11;
             ySwitch.setState(true);
             y = 10 + joyY * 11;
             e.setNewValue(computer.getVideo().getFloatingBus());
+            resume();
         }
     };
 

src/main/java/jace/tracker/PlaybackEngine.java

@@ -69,7 +69,7 @@ public class PlaybackEngine extends Computer {
             throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
         }
     };
-    Motherboard motherboard = new Motherboard(dummyComputer);
+    Motherboard motherboard = new Motherboard(dummyComputer, null);
     CardMockingboard mockingboard = new CardMockingboard(dummyComputer);
 
     public PlaybackEngine() {