My first thought is you may have W/C cabling or termination issues. Maybe try locking to AES instead ?
I don't know from where your ADAT comes, so hard to follow this issue. Nor do I know what your "console channel" is, so hard to make sense of this.
It is possible that there is a hardware issue with the clock circuitry, but this would tend to cause total failure rather than the symptoms you report. Hard to say.