I had set up log shipping from 2005 instance to 2008 instance. The only problem I had was connecting to the 2008 instance via the management studio on the server which had sql server 2005 installed.
So I used the management studio on the server with sql server 2008 to connect to both the instances. And I configured everything via 2008 management studio.
I would assume that Enterprise manager will not be able to connect to a SQL Server 2008 instance. So you can try using management studio 2008 instead.
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