Hi,
Not sure if this is a RAWCooked issue or a Media Conch issue, but I am guessing that it is just something in MediaConch having problems rather than a true conformance failure caused by RAWCooked.
I have a set of FFV1/MKV files that were created by RAWCooked and contain the embedded reversibility metadata, and it appears that on some of them this data is causing MediaConch's EBML implementation checker to read them as non-compliant. I made some gists with the metadata output of MediaConch for one of the affected files: