Ran into a problem configuring SCR here at a client, the client has an empty root domain with a child resource domain. Exchange is in the Child resource domain along with everything else. When I attempted to get configure SCR between two mailbox servers I got an error about SCR is not supported between servers in different domains. My first thought was to verify the machines were in the same domain and yes they are. I then tried the command from the target machine for the SCR (first time was from source) and got the same error.
I then went searching and found this:
http://blogs.technet.com/timmcmic/archive/2008/12/21/exchange-2007-sp1-ru5-error-regarding-replication-between-computers-in-different-domains-when-using-standby-continuous-replication-scr.aspx
Seems that Exchange 2007 SP1 Rollup 5 introduced this error and it was not fixed in Rollup 6 just released this month. The link has work some arounds for the problem and states it is schedule to be fixed in Rollup 7. Thanks to Tim McMichael for explaining this bug so I did not go crazy and start rebuilding or re-joining servers to domains.
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