sdj0103, where is your usercontrol defined? I think it's likely that you have some pages at application root that references this usercontrol in a separate folder, and that usercontrol references the masterpage in the root folder, therefore this causes the circular reference.
If this is the reason, you should consider moving masterpage file to a different folder than the root or usercontrol. Thus the pages and usercontrol can both depend on the masterpage batch assemblies without the circular reference.
If this does not solve your problem, could you send me your repro files so I can investigate?
Thanks,
Ting
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