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JOptionPane in JavaFX Making Window 'Not Respond'

I am building a JavaFX app and am using JOptionPane to display dialogs
One of the problems I've encountered is that creating a new dialog and not dismissing it within 5 or so seconds will cause the main JavaFX stage go into a 'Not Responding' state
Running the joptionpane code in a new thread works, but causes the dialog not to be modal, which is not suitable for the app i'm building
This is all running in Windows.
Any ways to fix the not responding problem would be greatly appreciated :)
EDIT: The code I use is (from the main JavaFX thread)
JOptionPane.showMessageDialog(null, "message here");
Perhaps null is causing the problem?

You can't just show a JoptionPane, which is a Swing component, from the FX thread. You have three options:
create a Swing application and place all the fx nodes in JFXPanels.
use FX nodes only, for example by using a modal stage or by using an external library such as ControlsFX (JavaFX 8 only but there are other libraries available that work with JavaFX 2)
place your JOptionPane in a SwingNode (JavaFX 8 only)
For 1 and 3 you need to be careful to create/modify the Swing components on the Swing EDT thread and the JavaFX nodes on the JavaFX thread (unless you merge the two with the new JVM option available in Java 8). And I'm not 100% sure how the modality week work if you mix Swing and JavaFX.
If you are creating a JavaFX application there is little reason not to choose 2.

Don't use JOptionPane in a JavaFX application, use a JavaFX Alert instead. Alert was introduced in Java 8u40.
Using JOptionPane in JavaFX may be problematic due to the reasons pointed out in assylias's answer.
See also:
No errors, but crashing - JOptionPane - JavaFX

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I'm creating an application to test my Java skills, and I am using NetBeans because of the GUI builder because I'm not quite used to laying GUI's out by hand yet (the GUI is in Swing). I have a simple login form, that if the login information is correct, disappears and is replaced with different GUI elements. How could I make the second page that replaces the login page with the GUI builder?

You probably want a CardLayout. However, this might be a dup of Java Swing: How can I implement a login screen before showing a JFrame?

Java Swing, create a panel over a window by its hwnd handler

I'm writing a java app and at some point I create a window using Windows API through JNI.
How can I create a jpanel over a part of that window so I can add gui to it in the java side?
If that's not possible, then can I create a window in java and set it's parent to the first
window to achieve a similar result?

Java Window in another Window

Multi-window applications often have a main-window, and all other windows are kind of 'parented' to it. Minimizing such a sub-window will hide its content and show the title-bar at the bottom-left of the screen. Also, these windows do not have their own Icon in the Task-bar, only the main-window does.
How can I make a window being attached this way to another window?
If that is possible, is it also possible without a referenfe to the actual main window?
#2: I'm embedding Java into such an application and I would like to be able to use awt or swing additionally to the native dialogs, which have this behavior by default.

See How to Use Internal Frames.

have look at JInternalFrames for MDI application
read Oracle tutorial, try code example

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I have written a swing application in Java and want to display the logo of the application at program start-up for a couple of seconds before the actual program GUI appears. How do you think I can do this in swing?

A built-in Splash-Screen Functionality was added in Java SE 6, take a look here .

You can use SplashScreen: SplashScreen.getSplashScreen().setImageURL(imageURL)
If it does not meet your requirements for some reason you can either create instance of java.awt.Window or javax.swing.JWindow and put image at the middle of the window. Use Timer to disappear this window after specific timeout.
You can also use Frame or JFrame and call its f.setUndecorated(false)