WMP uses a different sound rendering method to produce the audio (DirectSound), we rely on the standard Windows drivers (MME/WDM) to render sound. It's possible in this instance that DirectSound is doing something extra to convert the file into a playable format, and the standard sound drivers are possibly not capable of doing the same thing.
to confirm is this "theory" is true or false, if anyone wants to give us a sample file that doesnt work, you can send it to me