Even if the in_reply_to_status_id isn't being set automatically, the in_reply_to_user_id *is*, so you can still see what user it was in reply to through the API even if the client didn't provide the field when posting the update.
It's very disconcerting to attempt to view a conversation and have it completely broken because twitter guessed at the wrong status, and this change was a long time coming. I hope that clients can update quickly and follow the specs laid out in the API.
