Essentially, BA needs to make sure there's enough fare bucket headroom to get anyone who's on a cheaper I fare in Business onto their feeder flight into LHR or LGW in Club Europe, so the system defaults to booking into J class for the connecting flight as that's never likely to run out except in very extreme circumstances (and they can just keep creating more up to the physical capacity of the CE cabin).

This is a high enough fare bucket that it attracts free seat selection (and, happily, more Avios).

As you are travelling in WT (domestic) then WTP (TATL) on the flights to JFK this does not apply for that direction, hence the difference.

It's deliberate, and not (for once) flaky IT. Your seat selection will stick.