Upgrade to 5.3 causes Nullpointer Exception and many features broken

I performed an upgrade from 5.2.3 to 5.3 and after the upgrade I get NullPointer exception in the logs ("currentApplication").

New notifications on top right corner not working.
Jira macros not working
lucidchart integration broken

All with the same exception about "current Application" being null.

2013-10-22 15:37:08,954 INFO [scheduler_Worker-3] [atlassian.crowd.directory.DbCachingRemoteDirectory] synchroniseCache INCREMENTAL synchronisation complete for directory [ 21495809 ] in [ 39ms ]
2013-10-22 15:37:23,155 ERROR [http-8443-58] [mywork.host.rest.ExceptionLogger] toResponse Exception thrown from resource
– url: /rest/mywork/latest/notification/nested | userName: xxxyyyzzz| referer: https://www.example.com/plugins/servlet/notifications-miniview
java.lang.NullPointerException: currentApplication
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:204)
at com.atlassian.applinks.core.auth.trusted.TrustedApplicationsRequestFactory.<init>(TrustedApplicationsRequestFactory.java:31)
at com.atlassian.applinks.core.auth.trusted.TrustedAppsAuthenticationProviderPluginModule$1.getRequestFactory(TrustedAppsAuthenticationProviderPluginModule.java:84)
at com.atlassian.applinks.core.auth.ApplicationLinkRequestFactoryFactoryImpl.createImpersonatingRequestFactory(ApplicationLinkRequestFactoryFactoryImpl.java:138)
at com.atlassian.applinks.core.auth.ApplicationLinkRequestFactoryFactoryImpl.createImpersonatingRequestFactory(ApplicationLinkRequestFactoryFactoryImpl.java:125)
at com.atlassian.applinks.core.auth.ApplicationLinkRequestFactoryFactoryImpl.getApplicationLinkRequestFactory(ApplicationLinkRequestFactoryFactoryImpl.java:96)
at com.atlassian.applinks.core.link.DefaultApplicationLink.createAuthenticatedRequestFactory(DefaultApplicationLink.java:118)
at com.atlassian.mywork.host.service.AppLinkHelper.execute(AppLinkHelper.java:59)
at com.atlassian.mywork.host.service.AppLinkHelper.execute(AppLinkHelper.java:42)
at com.atlassian.mywork.host.service.ClientServiceImpl.verifyAuth(ClientServiceImpl.java:147)
at com.atlassian.mywork.host.rest.NotificationResource.findByUserNested(NotificationResource.java:102)
at sun.reflect.GeneratedMethodAccessor2071.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$ResponseOutInvoker$1.invoke(DispatchProviderHelper.java:234)
at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$1.intercept(DispatchProviderHelper.java:100)
at com.atlassian.plugins.rest.common.interceptor.impl.DefaultMethodInvocation.invoke(DefaultMethodInvocation.java:61)
at com.atlassian.plugins.rest.common.expand.interceptor.ExpandInterceptor.intercept(ExpandInterceptor.java:38)
at com.atlassian.plugins.rest.common.interceptor.impl.DefaultMethodInvocation.invoke(DefaultMethodInvocation.java:61)
at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper.invokeMethodWithInterceptors(DispatchProviderHelper.java:132)