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Since you have changed the configuration of the Domino server underlying Sametime, the Sametime installation has become "confused" and no longer executes as it did when the system was a single server install. You are sort of on the right track with registry settings, but there is a lot more than OS considerations when installing a Sametime system.
The solution to your problem is to uninstall Sametime. Place the original Domino servers notes.ini back into the program path (it would now be in data, data1, data2, etc., so it needs to go back into the program path). Then re-install Sametime.
Once the installation is complete, move the notes.ini back into the correct data location and check the "directory=" line to ensure it is pointing to the correct partition.
Restart your server, and Sametime should start as part of the appropriate Domino partition.
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