Every JavaFX application I've run throws two NullPointerExceptions. They don't prevent or even affect the execution of the projects, and I can only see them if I run my applications in debug mode. I'm even having this issue with the HelloWorld sample from Oracle and this minimal program:
public class JavaFXTSample extends Application {
    @Override
    public void start(Stage primaryStage) throws Exception {
        StackPane iAmRoot = new StackPane();
        Scene scene = new Scene(iAmRoot, 300, 250);
        primaryStage.setScene(scene);
        primaryStage.show();
    }
    public static void main (String[] args) {
        launch(args);
    }
}
Here is the stack trace of the first error:
 Thread [main] (Suspended (exception NullPointerException)) 
    SystemProperties.setVersions() line: 81 [local variables unavailable]   
    SystemProperties.lambda$static$28() line: 67    
    30621981.run() line: not available  
    AccessController.doPrivileged(PrivilegedAction<T>) line: not available [native method]  
    SystemProperties.<clinit>() line: 64    
    LauncherImpl.startToolkit() line: 668   
    LauncherImpl.launchApplicationWithArgs(String, String, String[]) line: 337  
    LauncherImpl.launchApplication(String, String, String[]) line: 328  
    NativeMethodAccessorImpl.invoke0(Method, Object, Object[]) line: not available [native method]  
    NativeMethodAccessorImpl.invoke(Object, Object[]) line: not available   
    DelegatingMethodAccessorImpl.invoke(Object, Object[]) line: not available   
    Method.invoke(Object, Object...) line: not available    
    LauncherHelper$FXHelper.main(String...) line: not available 
And here is the second:
Thread [JavaFX Application Thread] (Suspended (exception NullPointerException)) 
    PropertyHelper.lambda$getBooleanProperty$514(String) line: 39   
    7164036.run() line: not available   
    AccessController.doPrivileged(PrivilegedAction<T>) line: not available [native method]  
    PropertyHelper.getBooleanProperty(String) line: 37  
    Parent.<clinit>() line: 87  
    JavaFXTSample.start(Stage) line: 16 
    LauncherImpl.lambda$launchApplication1$162(AtomicBoolean, Application) line: 863    
    2266602.run() line: not available   
    PlatformImpl.lambda$runAndWait$175(Runnable, CountDownLatch) line: 326  
    32251660.run() line: not available  
    PlatformImpl.lambda$null$173(Runnable) line: 295    
    11305869.run() line: not available  
    AccessController.doPrivileged(PrivilegedAction<T>, AccessControlContext) line: not available [native method]    
    PlatformImpl.lambda$runLater$174(Runnable, AccessControlContext) line: 294  
    30052382.run() line: not available  
    InvokeLaterDispatcher$Future.run() line: 95 
    WinApplication._runLoop(Runnable) line: not available [native method]   
    WinApplication.lambda$null$148(int, Runnable) line: 191 
    32126786.run() line: not available  
    Thread.run() line: not available    
What's more, if I remove any instance of iAmRoot and scene (so start() just reads primaryStage.show();), the second error doesn't occur. Why is this happening?
I've been able to find this question before (JavaFX application throws NullPointerException at startup), but noone seems to have resolved it, and it was asked over 2 years ago.
If it helps, I'm running Eclipse 4.5.2 on Windows 7 Professional, and I don't think I'm using FXML at all.
EDIT:
for what it's worth, I can't find the source code for the second error, but I found JavaFX's code for the method which throws the first error (line 81):
58  private static final String versionResourceName =
59       "/com/sun/javafx/runtime/resources/version.properties";
...
78 private static void setVersions() {
79     int size;
80     InputStream is =
81         SystemProperties.class.getResourceAsStream(versionResourceName);
82     try  {
83         size = is.available();
84         
85         byte[] b = new byte[size];
86         int n = is.read(b);            
87         String inStr = new String(b, "utf-8");
88         SystemProperties.setFXProperty("javafx.version",
89             getValue(inStr, "release="));
90 
91         SystemProperties.setFXProperty("javafx.runtime.version",
92             getValue(inStr, "full="));
93 
94      } catch (Exception ignore) {
95      }
96 }
 
    