Hi,
We had the same problem.
What we found was that Sap has a new Login Module called HeaderVariableLoginModule which you have to create using the class com.sap.security.core.server.jaas.HeaderVariableLoginModule. You can do this in NWA -> Configuration -> Authentication and Single Sign-On -> Login Module, then click on the create button and fill out the fields with the information i just gave you.
The list of Login Modules should now include HeaderVariableLoginModule, which you can configure by selecting the row of this module, and adding two options- ume.configuration.active=true and Header=REMOTE_USER.
It appears that this Login Module is covertly delivered as a class in every Netweaver version >= 7.0.
Good luck,
Steven McElwee, Duke University
PS- I tried to attach a word document that shows the procedure for this, but this system rejected it. I can email it you if you let me know where to send it. In our case we used "Header=uid" rather than "Header="REMOTE_USER".