I have Arcgis server 9.3.1 set up with SQL server authentication and token service enabled. When i access a map service with just token passed in the Url (http: //myserver/arcgis/rest/services?token=....), i get authenticated properly. For example, the following url works.
When requesting html output explicitly via url parameter (http: //myserver/arcgis/rest/services?token=....&f=html), this also works without any problem.