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Seems x64 CLR dlls do not display mscoree.dll as a dependency. So now it seems CLR dlls are not getting enumerated properly. Please check the x64 build's dependencies.
So in my branch I changed the ClrPhLib to detect CLR dlls based on COM DESCRIPTOR on the dll file. Now it can display the CLR dependencies on x64 binaries.
Please check this and let me know if there is any thing more I can do to help fix this issue. I'd be happy to help.