I have an update. I discovered that the problem is only effecting 88.2 kHz content. That ended up being most of my library because I had Roon set to upsample all 44.1 kHz content to 88.2 kHz. I can work around this by not having any content upsampled to 88.2 kHz and having any 88.2 kHz native content upsampled to 96 kHz, but if you any explanation for why this is happening I would appreciate it.