Did you try to get the seat assigned on the DL flight via the Flying Blue website (after logging in)? As I am not an FB member, I am not sure whether this is possible, but I assume if it is, then you should be able to select the EC seat.

I had a somewhat similar experience. I have an award seat booked via OK Plus which include a DL flight (jackpot I know... but in Y, of course, since booking J on a DL transcon with partner miles would be nothing short of a miracle). I don't have an elite status with OK Plus, but I have one with DL. Interestingly, even after adding the ticketed award reservation (which was apparently booked using my OK Plus FF #) to MyDelta for several weeks I kept seeing the popup to pay for the EC seat when I try to select it... until it suddenly disappeared and the system allowed me to select such seat for free. Nothing really changed with my reservation during this time, but I guess my status with DL finally overwrote the OK Plus status.

By the way, I think for the first few weeks even Preferred seats on DL were not selectable