When you enable Profiling through the Administration interface in JIRA, it doesn't automatically reload the components already registered with the ComponentManager. Because it does not do this, the components are not wrapped by the Profiling dynamic proxy (TimerInvocationHandler), and thus all the implicit profiling that is supposed to occur (timing method invocations and so on) doesn't. Note that explicit profiling works as expected.

One way to get the implicit profiling to work after enabling profiling is to restore an XML backup of your instance's data. This operation reloads the ComponentManager and thus correctly wraps the components with the dynamic proxy.