Only the Check overloads allow you to return problems. Although you can still add problems to the Problems property in other methods, FxCop is not aware of this property, and only looks at ProblemCollection returned from the Check methods.
You can actually get access to all the assemblies in analysis by looking at the RuleUtilities.AnalysisAssemblies property. So simply iterate over that in the assembly check to determine any problems.
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