@smallfat: For your case, you are playing Rune on C2 that I would like to know what way/where you are transporting the digital signal to?
1) to Hifi Shield dac board?
2) to hdmi port?
3) to usb port connected to an external USB DAC?
My case Rune/C2 out to usb port connected to an external USB DAC (SMSL M8, that played perfectly with signal from Pi 2) the sound for 16/44.1 is very distorted. It is very strange it played 24/192 perfectly. I keep dsd aside since it is still not popular now at least for us.
I installed Ubuntu MATE that I tried with Audacious it played 16/44.1 perfectly.
I tried playing 16/44.1 in terminal window command "aplay <wav or flac files>" it played perfectly.
I spent time much myself to find out but nothing much found now since I am not a linux guy. I am sorry if this share may make some inconvenience for you.
My best regards.
Have a nice day !