So, at the moment it looks like the issues may not have been roon.
My QNAP NAS recently got updates and it looks like the version of ffmpeg installed by QNAP is rather pathetic.
I followed the instructions here
and this seems to have fixed the issue.
The QNAP installed version of the ffmpeg library was 240K in size, whereas the one from QNAP Club is over 75MB - a massive change.
After updating the ffmpeg library and restarting Roon I now seem to have a stable Roon again.
But… Why would this affect FLACs and other codecs? Any thoughts?
I want to keep this open for now and see how things go today.
I’ll keep you posted.