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We just went though this issue with our RoD environment. BMC was unable to get the Windows Authentication to work because our RoD environment is on Linux Servers. We had to change our SCCM Windrows Server to Mixed Mode Authentication and then we were able to add a SQL Authenticated account to SCCM and that worked for the install of the SCCM Connector tool.
Hope this helps,
We are in the same situation. Will have to use SQL account instead of windows authentication due to the linux hosts.