De acordo com esta discussão , os únicos codecs que os aplicativos WinRT podem usar devem ser fornecidos pela Microsoft ou incluídos no aplicativo. Os aplicativos WinRT não podem usar codecs instalados a partir da área de trabalho, e parece não haver nenhuma maneira de disponibilizar um codec de terceiros para todos os aplicativos WinRT.
This behavior is by design. In order for you to use your FLAC MF codec from within the context of your Windows store app you will need to modify the codec to work in the WinRT environment. You will then need to ship the codec with your application rather than rely on a desktop installation.
Editar : Mais informações de @Bala Sivakumar , gerente de programa da Microsoft Equipe de Plataforma MM
The reason for this is that Windows 8 is designed to run on low-power devices where software decoding is not desirable. Therefore only codecs that can be hardware accelerated are supported system-wide. Third party codecs can be made available in some cases - where the graphics card manufacturer supports hardware acceleration of the codec and ships support in the driver. Such codecs are signed by Microsoft to allow for system-wide use.