We just finished a pretty major change to how the NHibernate Profiler interacts with NHibernate. That change was mostly driven out of the desire to fully support running under the client profile and to allow us to support the new logging infrastructure in NHibernate 3.x.
The good news, this is done , you can now use NH Prof from the client profile, and you don’t need to do anything to make it work for NHibernate 3.x.
The slightly bad news is that if you were relying on log4net conifguration to configure NH Prof, there is a breaking change that affects you. Basically, you need to update your configuration. You can find the full details on how to do this in the documentation.