Hy Tom,
I have the same issue since more than one month. I was investigating many time into this, since it is blocking my project. I started a forum entry here:
http://forums.asp.net/t/1946475.aspx?Duplicated+key+when+try+to+register+multiple+ObjectContexts+in+Dynamic+Data
It worked in previous versions.
There was a workaround (see http://blog.davidebbo.com/2011/01/using-dynamic-data-with-ef-code-first.html) but this does not help anymore for current versions.
In short: it is an ASP.Net bug. Since we cannot call DbContext directly (which would be distinguishable) and we have to call ObjectContext, and the internal dictionary for the MetaModel uses the type without namespace as key (i.e. always "ObjectType"), there is no way around it.
Luckily, the ASP.Net team is now investigating into it now. Keep informed on the mentioned forum page.
UPDATE MARCH 2014: The current version http://blogs.msdn.com/b/webdev/archive/2014/02/28/announcing-the-release-of-dynamic-data-provider-and-entitydatasource-control-for-entity-framework-6.aspx fixes the problem.