App Init behaviour different between IIS Restart and Application Initialisation

App Init behaviour different between IIS Restart and Application
Initialisation

I am using the IIS Application Initialisation module to warm-up an asmx
wed service.
I have implemented some warm-up code to ensure app application
initialisation successfully JIT's my asmx service in Global.asax
Application_Start event. This uses
System.Runtime.CompilerServices.RuntimeHelpers.PrepareMethod() to iterate
through all of the assemblies in the application (it also picks up all of
the assembly dependencies) to ensure that the first call to the service is
as fast as possible.
When I obeserve this behaviour utilising "net stop w3svc & net start
w3svc" I can see (via logging) that ALL of the assemblies are JIT'ted and
the first call to the service is fast as expected.
However, when the application pool is automatically recycled on its
configured time schedule (03:00:00) the log shows only the directly
referenced assemblies are JIT'ted, not the dependencies that also sit in
the folder.
This is resulting in an unacceptable overhead on the first call to the
service.
The App Init performs exactly as expected in all other respects but why
does the IIS re-cycle of the Application Pool only JIT compile the
directly referenced assemblies and not its dependencies?