dotPeek and NGEN native image files

I've setup my dotPeek configuration to decompile .NET framework assemblies but I've noticed certain ones fail to decompile because it appears that the application is loading native images instead of IL assemblies. The ones I'm having trouble with are:
System.IO.dll
System.Runtime.dll

When dotPeek attempts to generate pdb files for the symbol server instead of looking for System.IO.dll it's looking for System.IO.ni.dll, which from what I understand isn't in the GAC but in a separate NIC (native image cache) instead. In any case I'm not interested in decompiling the native image file because, well, you can't. How do I coerce dotPeek into using the System.IO.dll (which does appear to be in the GAC) rather than the System.IO.ni.dll?

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Some problem here with EntityFramework.ni.dll.

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Same for System.Threading(.ni).dll, Reflection, Collections, Linq, Threading, ...

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