If you build SampleApp with the latest (i.e. May 25th's) JWrapper, it won't start on windows. According to SampleApp-SampleApp..log, it appears to be trying to load a MacOSX class (JWOSXEventListener) at runtime:
87342876 (+ 0) STDOUT test
87342876 (+ 0) STDERR test
87342876 (+ 0) [LogFolderCleaner] Keeping Wrapper-2015-05-26-17-42-08-852.log
87342876 (+ 0) [LogFolderCleaner] Keeping SampleApp-SampleApp-2015-05-26-17-42-22-876.log
87342876 (+ 0) [LogFolderCleaner] Keeping GenericUpdater-2015-05-26-17-42-18-945.log
87342876 (+ 0) [JWrapper] App Bundle Name: SampleApp
87342876 (+ 0) [JWrapper] App Bundle Version: 00036171806
87342876 (+ 0) [JWrapper] Virtual App: SampleApp
87342876 (+ 0) [JWrapper] Update URL: http://0.0.254.254/
87342876 (+ 0) [JWrapper] App Folder: C:\Users\christop\AppData\Roaming\JWrapper-SampleApp\JWrapper-SampleApp-00036171806-complete
87342876 (+ 0) [JWrapper] JRE: C:\Users\christop\AppData\Roaming\JWrapper-SampleApp\JWrapper-Windows32JRE-00036170991-complete
87342876 (+ 0) [JWrapper] JRE Version: 1.7.0_05
87342876 (+ 0) [JWrapper] Proxy: null
87342876 (+ 0) [EDT Exception Printer] Catching all EDT and uncaught exceptions and printing
87342892 (+ 16) [JWrapperNative] Detected 32-bit architecture
87342892 (+ 0) [JWrapperNative] Detected Windows OS
87342892 (+ 0) [JWrapper] Is Process DPI Aware: true
87342892 (+ 0) [JWrapper] sun.java2d.dpiaware: null
87342892 (+ 0) [JWDetectedProxy] No proxy configuration found to load.
87342892 (+ 0) JVM Option: -Xmx256m
87342892 (+ 0) [JWrapper] JVM Home: C:\Users\christop\AppData\Roaming\JWrapper-SampleApp\JWrapper-Windows32JRE-00036170991-complete
87342908 (+ 16) [PermissionsUtil] Setting permissions for C:\Users\christop\AppData\Roaming\JWrapper-SampleApp\JWApps\JRE-LastSuccessfulOptions-JWrapper-Windows32JRE-00036170991-complete to F
87342908 (+ 0) [PermissionsUtil] Finished setting permissions.
87342908 (+ 0) [JWrapper] Wrote JVM Options OK
87342908 (+ 0) [AWT/Swing Exception] (STDERR) Exception on thread main (java.lang.NoClassDefFoundError: jwrapper/hidden/events/JWOSXEventListener)
87342923 (+ 15) java.lang.NoClassDefFoundError: jwrapper/hidden/events/JWOSXEventListener
87342923 (+ 0) at java.lang.Class.forName0(Native Method)
87342923 (+ 0) at java.lang.Class.forName(Unknown Source)
87342923 (+ 0) at jwrapper.JWrapper.main(JWrapper.java:290)
87342923 (+ 0) Caused by: java.lang.ClassNotFoundException: jwrapper.hidden.events.JWOSXEventListener
87342923 (+ 0) at java.net.URLClassLoader$1.run(Unknown Source)
87342923 (+ 0) at java.net.URLClassLoader$1.run(Unknown Source)
87342923 (+ 0) at java.security.AccessController.doPrivileged(Native Method)
87342923 (+ 0) at java.net.URLClassLoader.findClass(Unknown Source)
87342923 (+ 0) at java.lang.ClassLoader.loadClass(Unknown Source)
87342923 (+ 0) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
87342923 (+ 0) at java.lang.ClassLoader.loadClass(Unknown Source)
87342923 (+ 0) ... 3 more
This is where JWrapper loads the app class, the exception is due to the class failing to load, this is due to a bug in the sample app code which references a class which has been moved in the latest JW build.