Have been able to duplicate this with two server setups. Wondering if anyone has encountered this problem and found a work around?
ArcGIS Server 10.1 sp1, ArcGIS Desktop 10.1 sp1
Using a WebAdapter, or directly to the GIS server
Configuration Settings
User Store: 10.0 SQL Server (This is a aspnet user store in SQL)
Role Store: 10.0 SQL Server
Authentication Tier GIS Server
Authentication Mode: ArcGIS Tokens
If I connect to the rest and log in with a user I see the folders/services that user has permissions to see. If I make an ArcCatatlog connection with that user there is nothing, not even public folders or services available.
It is known bug in ArcGIS server 10.1 SP1
Please refer : NIM086160 Unable to make a user connection to ArcGIS Server from ArcGIS Desktop with a user from 10.0 SQL user or role store.
I faced the same issue and waiting for ESRI-ArcGIS Server -Patch to resolve