From the docs for SecurityManager (1.4.2):

 Note that the checkPermission method with just a single permission
argument always performs security checks within the context of the
currently executing thread. Sometimes a security check that should be
made within a given context will actually need to be done from within a
different context (for example, from within a worker thread). The
getSecurityContext method and the checkPermission  method that includes
a context argument are provided for this situation. The
getSecurityContext method returns a "snapshot" of the current calling
context. (The default implementation returns an AccessControlContext
object.) A sample call is the following:

   Object context = null;
   SecurityManager sm = System.getSecurityManager();
   if (sm != null) context = sm.getSecurityContext();

The checkPermission method that takes a context object in addition to a
permission makes access decisions based on that context, rather than on
that of the current execution thread. Code within a different context
can thus call that method, passing the permission and the
previously-saved context object. A sample call, using the
SecurityManager sm obtained as in the previous example, is the following:

   if (sm != null) sm.checkPermission(permission, context);

Perhaps you can code your SecurityManager to differentiate based on the
context that it is in?

Good luck!

Rogan