An issue that came up five or six years ago with some DACs was that their XMOS USB firmware simply copied an example bit of firmware code that didn’t take into account changes in sample rate or sample width, and when such a change occurred, the DAC would just skip over the subsequent tracks. Roon made a change to mitigate this, then most manufacturers updated their firmware to fix it.
The workaround was to tell Roon to upsample all tracks to a standard depth and rate for that device.
I don’t know if your problem is related, but given that Roon seems to be working with everything else, I’d suspect something with the amp or its DAC.