If I understand correctly, you have one specific RFC that has a connection to earth somewhere, despite the installation earth & bonding connections all being disconnected?
As others have mentioned, I'm not totally understanding why this is a problem? I'm assuming nothing is tripping, and you just want to know why, rather than needing to disconnect this other earth? Normally I'd just move on.
Assuming you really do need or want to know, then can you not just split the RFC into two, and find which half is still earthed. Then repeat with the earthed bit, until you narrow it down? Just like looking for any other fault on an RFC?
And when you say earthed, are you measuring a resistance to the suppliers' earth? If so, what value (from each end of the RFC)? Or did I recall seeing you are measuring Zs values on this RFC (with main earth and bonding disconnected)?