I may be wrong but it sounds like you are talking about bug NIM083117
Synopsis
A 10.1 ArcGIS for Server site does not support multiple security stores. 10.0 had support for multiple security stores.
Additional Status Information
N/A
Alternate Solution
At 10.1, the ArcGIS for Server security model does not support the use of two identity stores with a single ArcGIS Site. For customers who must use multiple identity stores, we suggest creating two ArcGIS Sites, with each site configured to use a different identity store. Please have the customer contact their ESRI Account Manager to obtain licensing information for this type of ArcGIS Server configuration.
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To my knowledge this bug is not fixed in 10.2