I have the same problem (at XI 3.0 sp9). After following the steps in the note 764176 the problem still exists. Any other suggestions.
When I try and generate communcation channels automatically I get the following message for the four base channel types -
Unable to create communication channel: Attempt to access the 1 requested objects on 1 failed. Detailed information: com.sap.aii.ib.core.roa.RoaObjectAccessException: Attempt to read object Adapter Metadata XI | http://sap.com/xi/XI/System (SAP BASIS 6.40), type AdapterMetaData from application REPOSITORY on system REPOSITORY failed. Object does not exist. Detailed informatio n: Adapter Metadata XI | http://sap.com/xi/XI/System not found
With a little further digging (note 742694) I have found that the SAP BASIS 6.40 namespace in the repository is not populated. Which is what the error says if you know how to read it.
Simple fix - The imported XI content has to match the supportpack verion, follow the steps in Note 705541
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