Encore CS6 always transcodes 1440x1080 h264 video imports

If I encode an interlaced 1920x1080 files with x264 I can import it into encore and it will not transcode. If I import a 1440x1080 file into encore it always wants to re-transcode. The only clue I have is that it does not get the pixel aspect ratio right and I have to force it to be 4:3. Unfortunatly Encore does not re-evaluate for transcode when I do this. If I import the file into premiere pro the correct par is detected. So there seems to be a difference between how premiere and encore determine the par.
The file is a raw h264 video 1440x1080i50 with the sar set to 4:3.
If I use the premiere pro encoder that works correctly. Please can someone tell me how I can correct for this problem. I want to use x264 as it is the most superior encoder on the planet.
Regards Trevor

Please note the tool I used was h264info to fix the file.
I did try the revert to original but that did not work.
Mediainfo:
General
Complete name                            : C:\Users\trevor\bluray\stockholm\stockholm5.264
Format                                   : AVC
Format/Info                              : Advanced Video Codec
File size                                : 213 MiB
Overall bit rate mode                    : Variable
Video
Format                                   : AVC
Format/Info                              : Advanced Video Codec
Format profile                           : [email protected]
Format settings, CABAC                   : Yes
Format settings, ReFrames                : 4 frames
Bit rate mode                            : Variable
Bit rate                                 : 30.0 Mbps
Maximum bit rate                         : 35.0 Mbps
Width                                    : 1 440 pixels
Height                                   : 1 080 pixels
Display aspect ratio                     : 16:9
Frame rate                               : 25.000 fps
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : MBAFF
Bits/(Pixel*Frame)                       : 0.772
Writing library                          : x264 core 125 r2200 999b753
Encoding settings                        : cabac=1 / ref=5 / deblock=1:0:0 / analyse=0x3:0x113 / me=umh / subme=8 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=36 / lookahead_threads=6 / sliced_threads=0 / slices=4 / nr=0 / decimate=1 / interlaced=tff / bluray_compat=1 / constrained_intra=0 / bframes=3 / b_pyramid=1 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=1 / weightp=0 / keyint=25 / keyint_min=1 / scenecut=40 / intra_refresh=0 / rc_lookahead=25 / rc=2pass / mbtree=1 / bitrate=30000 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / vbv_maxrate=35000 / vbv_bufsize=30000 / nal_hrd=vbr / ip_ratio=1.40 / aq=1:1.00
Color primaries                          : BT.709-5, BT.1361, IEC 61966-2-4, SMPTE RP177
Transfer characteristics                 : BT.709-5, BT.1361
Matrix coefficients                      : BT.709-5, BT.1361, IEC 61966-2-4 709, SMPTE RP177
x264 declares scan type as MBAFF but mainconcept sets it to Interlaced. Mainconcept also has a scan order: Top Field First. I have not found any way to change these in the file. I notice that there is a x286Pro plugin for Premiere which seems to have fixed alot of problems in Premiere.

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