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This is expected behavior and the following enhancement request has been logged.
NIM008501: Enhance the Cache functionality so that when creating a cache from a service with �??group layers�??, currently only the group layer themselves can be selected for multi-layer - enhance to allow the individual layers within the group layer to be selected
One thing to consider is that there is little to no advantage of using multilayer cache with a Web Application. Multilayer cache is intended to be consumed by desktop products such as ArcMap or a custom Engine application.
For additional help on designing services for web applications, check out this Blog Post.
Hope that helps!