I think I attached the wrong stacktrace. It should not be the one stopping at the breakpoint. Probability to get a stacktrace like this is higher if you create a stacktrace while processing:

Thread [main] (Suspended)
owns: JarFile (id=4504)
System.arraycopy(Object, int, Object, int, int) line: not available [native method]
Arrays.copyOf(byte[], int) line: 3237
ZipCoder.getBytes(String) line: 89
JarFile(ZipFile).getEntry(String) line: 311
JarFile.getEntry(String) line: 240
JarFile.getJarEntry(String) line: 223
URLClassPath$JarLoader.getResource(String, boolean) line: 1005
URLClassPath$JarLoader.findResource(String, boolean) line: 983
URLClassPath.findResource(String, boolean) line: 188
URLClassLoader$2.run() line: 569
URLClassLoader$2.run() line: 567
AccessController.doPrivileged(PrivilegedAction<T>, AccessControlContext) line: not available [native method]
Launcher$AppClassLoader(URLClassLoader).findResource(String) line: 566
Launcher$AppClassLoader(ClassLoader).getResource(String) line: 1093
Launcher$AppClassLoader(URLClassLoader).getResourceAsStream(String) line: 232
AccessorInjector.tailor(String, String, String...) line: 113
AccessorInjector.prepare(Class, String, String, String...) line: 79
OptimizedAccessorFactory.get(Field) line: 165
Accessor$FieldReflection<BeanT,ValueT>.optimize(JAXBContextImpl) line: 253
TransducedAccessor$CompositeTransducedAccessorImpl<BeanT,ValueT>.<init>(JAXBContextImpl, Transducer<ValueT>, Accessor<BeanT,ValueT>) line: 231
TransducedAccessor<BeanT>.get(JAXBContextImpl, RuntimeNonElementRef) line: 173
SingleElementLeafProperty<BeanT>.<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 83
GeneratedConstructorAccessor15.newInstance(Object[]) line: not available
DelegatingConstructorAccessorImpl.newInstance(Object[]) line: 45
Constructor<T>.newInstance(Object...) line: 422
PropertyFactory.create(JAXBContextImpl, RuntimePropertyInfo) line: 124
ClassBeanInfoImpl<BeanT>.<init>(JAXBContextImpl, RuntimeClassInfo) line: 171
JAXBContextImpl.getOrCreate(RuntimeClassInfo) line: 481
JAXBContextImpl.getOrCreate(RuntimeTypeInfo) line: 500
ArrayElementNodeProperty<BeanT,ListT,ItemT>(ArrayElementProperty<BeanT,ListT,ItemT>).<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 108
ArrayElementNodeProperty<BeanT,ListT,ItemT>.<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 58
GeneratedConstructorAccessor13.newInstance(Object[]) line: not available
DelegatingConstructorAccessorImpl.newInstance(Object[]) line: 45
Constructor<T>.newInstance(Object...) line: 422
PropertyFactory.create(JAXBContextImpl, RuntimePropertyInfo) line: 124
ClassBeanInfoImpl<BeanT>.<init>(JAXBContextImpl, RuntimeClassInfo) line: 171
JAXBContextImpl.getOrCreate(RuntimeClassInfo) line: 481
JAXBContextImpl.getOrCreate(RuntimeTypeInfo) line: 500
ArrayElementNodeProperty<BeanT,ListT,ItemT>(ArrayElementProperty<BeanT,ListT,ItemT>).<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 108
ArrayElementNodeProperty<BeanT,ListT,ItemT>.<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 58
GeneratedConstructorAccessor13.newInstance(Object[]) line: not available
DelegatingConstructorAccessorImpl.newInstance(Object[]) line: 45
Constructor<T>.newInstance(Object...) line: 422
PropertyFactory.create(JAXBContextImpl, RuntimePropertyInfo) line: 124
ClassBeanInfoImpl<BeanT>.<init>(JAXBContextImpl, RuntimeClassInfo) line: 171
JAXBContextImpl.getOrCreate(RuntimeClassInfo) line: 481
JAXBContextImpl.getOrCreate(RuntimeTypeInfo) line: 500
ArrayElementNodeProperty<BeanT,ListT,ItemT>(ArrayElementProperty<BeanT,ListT,ItemT>).<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 108
ArrayElementNodeProperty<BeanT,ListT,ItemT>.<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 58
GeneratedConstructorAccessor13.newInstance(Object[]) line: not available
DelegatingConstructorAccessorImpl.newInstance(Object[]) line: 45
Constructor<T>.newInstance(Object...) line: 422
PropertyFactory.create(JAXBContextImpl, RuntimePropertyInfo) line: 124
ClassBeanInfoImpl<BeanT>.<init>(JAXBContextImpl, RuntimeClassInfo) line: 171
JAXBContextImpl.getOrCreate(RuntimeClassInfo) line: 481
JAXBContextImpl.getOrCreate(RuntimeTypeInfo) line: 500
SingleElementNodeProperty<BeanT,ValueT>.<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 100
GeneratedConstructorAccessor14.newInstance(Object[]) line: not available
DelegatingConstructorAccessorImpl.newInstance(Object[]) line: 45
Constructor<T>.newInstance(Object...) line: 422
PropertyFactory.create(JAXBContextImpl, RuntimePropertyInfo) line: 124
ClassBeanInfoImpl<BeanT>.<init>(JAXBContextImpl, RuntimeClassInfo) line: 171
JAXBContextImpl.getOrCreate(RuntimeClassInfo) line: 481
JAXBContextImpl.getOrCreate(RuntimeTypeInfo) line: 500
ArrayElementNodeProperty<BeanT,ListT,ItemT>(ArrayElementProperty<BeanT,ListT,ItemT>).<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 108
ArrayElementNodeProperty<BeanT,ListT,ItemT>.<init>(JAXBContextImpl, RuntimeElementPropertyInfo) line: 58
GeneratedConstructorAccessor13.newInstance(Object[]) line: not available
DelegatingConstructorAccessorImpl.newInstance(Object[]) line: 45
Constructor<T>.newInstance(Object...) line: 422
PropertyFactory.create(JAXBContextImpl, RuntimePropertyInfo) line: 124
ClassBeanInfoImpl<BeanT>.<init>(JAXBContextImpl, RuntimeClassInfo) line: 171
JAXBContextImpl.getOrCreate(RuntimeClassInfo) line: 481
JAXBContextImpl.<init>(Class[], Collection<TypeReference>, Map<Class,Class>, String, boolean, RuntimeAnnotationReader, boolean, boolean) line: 315
ContextFactory.createContext(Class[], Collection<TypeReference>, Map<Class,Class>, String, boolean, RuntimeAnnotationReader, boolean, boolean) line: 139
ContextFactory.createContext(Class[], Map<String,Object>) line: 117
NativeMethodAccessorImpl.invoke0(Method, Object, Object[]) line: not available [native method]
NativeMethodAccessorImpl.invoke(Object, Object[]) line: 62
DelegatingMethodAccessorImpl.invoke(Object, Object[]) line: 43
Method.invoke(Object, Object...) line: 497
ContextFinder.newInstance(Class[], Map, Class) line: 247
ContextFinder.newInstance(Class[], Map, String) line: 234
ContextFinder.find(Class[], Map) line: 441
JAXBContext.newInstance(Class[], Map<String,?>) line: 641
JAXBContext.newInstance(Class...) line: 584
MappingBinder(AbstractBinder).jaxb(XMLEventReader, Schema, Class<T>, Origin) line: 162
MappingBinder.doBind(XMLEventReader, StartElement, Origin) line: 57
MappingBinder(AbstractBinder).doBind(XMLEventReader, Origin) line: 102
MappingBinder(AbstractBinder).bind(InputStream, Origin) line: 57
InputStreamXmlSource.doBind(Binder, InputStream, Origin, boolean) line: 43
UrlXmlSource.doBind(Binder) line: 36
XmlMappingBinderAccess.bind(String) line: 59
MetadataSources.addResource(String) line: 274

So I guess the bad performance has something to do with constantly scanning the many big jar files for whatever is needed from them.