I have been testing the Premiere Pro CS6 H264 Blu-ray encoder with some HDV video 1440x1080i25 top field first and I have found that it always encodes as PAFF even when the MBAFF box is ticked. I analysed the stream with h264_parse and found that the mb_adaptive_frame_field_flag is set to 0 and that the pic_struct flag alternates between 1 and 2. These indicate that the encoder is using PAFF when the MBAFF flag is ticked.
The CS5 encoder does work as it sets the mb_adaptive_frame_field to 1 and the pic_struct to 3 which is correct for top field first.
There is another problem in that Premier pro does not recognise field order of correctly encoded MBAFF video. It reports tff video as progresive and bff as top top field first.