You are absolutely right, the problem is related to the changed format of the .rlinq.diagram file, required by the multiple diagram support and occurs the first time an existing rlinq file is opened. Unfortunately the only workaround is the one that you have already found out. The existing <entityDiagramsDiagram> root node should be enclosed with an <EntityDiagrams> node. This way the designer is able to serialize the formatting of more than one diagram.
This problem has already been fixed and the fix will be included in the next version of OpenAccess. I will update this thread once the build is available.
Thank you for reporting this issue and please excuse us for the inconvenience caused. Your Telerik points have been updated.
the Telerik team
Q3'12 SP1 of OpenAccess ORM packs Multi-Table Entities mapping support. Check it out.