If I define a namespace or include a reference to an assembly that defines a namespace that has the same name an existing namespace, ReSharper fails to see the root namespace for some reason. This is perhaps an odd one that I discovered when I included a reference to an assembly that has a System namespace in a lower hierarchy. In other words, the namespace in the referenced assembly is something like Foo.Bar.System. What's really odd is that ReSharper is no longer seeing the .NET Framework System namespace. I can type using System.IO and then reference FileInfo or Stream with no problem, but typing System.IO.FileInfo or System.IO.Stream doesn't give any intellisense on the System namespace and ReSharper claims the IO namespace doesn't exist.
Here's a quick 'n dirty way to reproduce the issue. When typing System, the only item in the intellisense list is Namespace and IO is highlighted in red as if it doesn't exist.
public class Foo
private System.IO.FileInfo _file;