This has to do with the order in which things happen in your Notes client.
Make sure the code you want to profile has not yet been loaded when you start Profiler. For example, if you want to profile the LotusScript code for a button, make sure that the form that the button is on is not open. Otherwise, Profiler will not recognize that the code is running.
Also because of the way the Notes client performs caching, you should restart the Notes client before running Profiler.
*This does not apply to running Profiler on Domino servers.