Hi, it is Feb 11, 2016 and I have this same issue. Status updates without media use the in_reply_to_status_id with no problem, but when I include media IDs in the submission then Twitter seems to ignore the in_reply_to_status_id. All across the internet there are threads with this problem but I never see any solution. This is not as trite as JS munging the INT value, because strings work with regular status updates utilizing in_reply_to_status_id but again do nothing when media is involved.
EDIT: After walking away and walking back I can see it was human error, a transposed character. Damn you dyslexia! Anyway, replying to tweets with media works very well using TwitterOAuth/api v1.1 in PHP