After upgrading to R901 removed the configuration and re-created it. Single Sign On works fine now!
The only "problem" to solve is the first time a user authenticates to the iNotes site it takes a very long time to authenticate. The domino console (debug) shows the SAML request is returned and the user is authenticated, however the ADFS site shows "page not found". The second attempt to access the site however is quick and successful.
In Domino I have increased the input and output time-out for a HTTP request, same results after restarting the server.
Is there any other time-out setting in ADFS or Domino to adjust?