Ive tried every ts fixer out there and even muxing to MP4 which rules out a container issue, And the files playback fine with the KISS PC link or through a network share so its not a corrupt file.
Here are the details of two files one plays for the full 2 hours the other for 50 minutes.
Incorrect time
General
ID : 1
Complete name : E:\Movies\Thriller\Bourne\The Bourne Ultimatum.mpg
Format : MPEG-TS
File size : 4.55 GiB
Duration : 1h 55mn
Overall bit rate : 5 653 Kbps
Maximum Overall bit rate : 35.5 Mbps
Video
ID : 4113 (0x1011)
Menu ID : 1 (0x1)
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4.1
Format settings, CABAC : Yes
Format settings, ReFrames : 8 frames
Duration : 1h 55mn
Bit rate : 4 621 Kbps
Nominal bit rate : 4 787 Kbps
Width : 1 280 pixels
Height : 528 pixels
Display aspect ratio : 2.40:1
Frame rate : 23.976 fps
Resolution : 8 bits
Colorimetry : 4:2:0
Scan type : Progressive
Bits/(Pixel*Frame) : 0.285
Stream size : 3.72 GiB (82%)
Writing library : x264 core 57 svn-699C
Encoding settings : cabac=1 / ref=5 / deblock=1:-3:-2 / analyse=0x1:0 / me=umh / fpel_cmp=sad / subme=7 / me-prepass=0 / brdo=1 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=0 / cqm=2 / deadzone=21,11 / chroma_qp_offset=0 / threads=6 / nr=0 / decimate=1 / mbaff=0 / bframes=3 / b_pyramid=1 / b_adapt=1 / b_bias=0 / direct=1 / wpredb=1 / bime=1 / keyint=250 / keyint_min=25 / scenecut=40(pre) / rc=2pass / bitrate=4787 / ratetol=1.0 / rceq='blurCplx^(1-qComp)' / qcomp=0.60 / qpmin=10 / qpmax=51 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / pb_ratio=1.3
Audio
ID : 4352 (0x1100)
Menu ID : 1 (0x1)
Format : AC-3
Format/Info : Audio Coding 3
Duration : 1h 55mn
Bit rate mode : Constant
Bit rate : 640 Kbps
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 48.0 KHz
Stream size : 528 MiB (11%)
Correct time
General
ID : 1
Complete name : H:\Action\Air Force One.mpg
Format : MPEG-TS
File size : 2.55 GiB
Duration : 2h 4mn
Overall bit rate : 2 927 Kbps
Maximum Overall bit rate : 35.5 Mbps
Video
ID : 4113 (0x1011)
Menu ID : 1 (0x1)
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4.1
Format settings, CABAC : Yes
Format settings, ReFrames : 5 frames
Duration : 2h 4mn
Bit rate : 2 276 Kbps
Nominal bit rate : 2 372 Kbps
Width : 1 280 pixels
Height : 528 pixels
Display aspect ratio : 2.40:1
Frame rate : 23.976 fps
Resolution : 8 bits
Colorimetry : 4:2:0
Scan type : Progressive
Bits/(Pixel*Frame) : 0.140
Stream size : 1.98 GiB (78%)
Writing library : x264 core 67 r1162M f7bfcfa
Encoding settings : cabac=1 / ref=5 / deblock=1

Audio
ID : 4352 (0x1100)
Menu ID : 1 (0x1)
Format : AC-3
Format/Info : Audio Coding 3
Duration : 2h 4mn
Bit rate mode : Constant
Bit rate : 448 Kbps
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 48.0 KHz
Stream size : 399 MiB (15%)