Error when implementing Global Timeout

Is there any architectural difference in how test runs in Junit when global timeout is set for test method and when its not set?

I am getting security errors(related to session) when I implement global timeout,even when the test is not timing out. What is the way to solve the issue? This isn't the complete stack trace but this is what I can share:

         sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
         sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
         java.lang.reflect.Method.invoke(Method.java:597)
         org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:45)
         org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
         org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
         org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
         org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:30)
         org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
 org.junit.internal.runners.statements.FailOnTimeout$StatementThread.run(FailOnTimeout.java:62)