I believe I have the same problem occuring in a different setup. OpenElec on a Haswell Nuc i3 will not play 44.1 KHz audio on my Pioneer AVX510 receiver in 1080p unless I upscale to 48KHz. In 720p it works.
Interestingly, a 88.2KHz audio file (FLAC) will not work either.
Hope this helps.