Hi EricV, I just specified "mpeg" as the extension, as I thought thats what was in it.  I can change it in TVHeadend, but I dont think it will make a difference.  I dont do any post processing, it is just what I put in the DVR config.
I seem to have isolated the skipping to a specific channel (one) on HD.
Here is another recording that has problems skipping.  This is the MediaInfo, and below is hte XBMC logs, which seem to describe errors with the audio?
> MEDIAINFO
> General
> ID                                       : 1 (0x1)
> Complete name                            : /home/macdoodles/Documents/MotoGP/MotoGP.2012-07-16.mpeg
> Format                                   : MPEG-TS
> File size                                : 14.9 GiB
> Duration                                 : 2h 42mn
> Overall bit rate mode                    : Variable
> Overall bit rate                         : 13.1 Mbps
> 
> Video
> ID                                       : 514 (0x202)
> Menu ID                                  : 1 (0x1)
> Format                                   : MPEG Video
> Format version                           : Version 2
> Format profile                           : Main@High
> Format settings, BVOP                    : Yes
> Format settings, Matrix                  : Custom
> Format settings, GOP                     : M=3, N=12
> Codec ID                                 : 2
> Duration                                 : 2h 42mn
> Bit rate mode                            : Variable
> Bit rate                                 : 12.0 Mbps
> Maximum bit rate                         : 90.0 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                                : Interlaced
> Scan order                               : Top Field First
> Compression mode                         : Lossy
> Bits/(Pixel*Frame)                       : 0.308
> Stream size                              : 13.6 GiB (92%)
> 
> Audio
> ID                                       : 672 (0x2A0)
> Menu ID                                  : 1 (0x1)
> Format                                   : AC-3
> Format/Info                              : Audio Coding 3
> Mode extension                           : CM (complete main)
> Codec ID                                 : 129
> Duration                                 : 2h 42mn
> Bit rate mode                            : Constant
> Bit rate                                 : 448 Kbps
> Channel(s)                               : 5 channels
> Channel positions                        : Front: L C R, Side: L R
> Sampling rate                            : 48.0 KHz
> Bit depth                                : 16 bits
> Compression mode                         : Lossy
> Delay relative to video                  : -611ms
> Stream size                              : 522 MiB (3%)
> Language                                 : English
> 06:37:08 T:3011709248  NOTICE: DVDPlayer: Opening: nfs://192.168.1.100/Multimedia/Recordings/MotoGP/MotoGP.2012-07-16.mpeg
> 06:37:08 T:3011709248 WARNING: CDVDMessageQueue(player)::Put MSGQ_NOT_INITIALIZED
> 06:37:08 T:2860575552  NOTICE: Thread CDVDPlayer start, auto delete: false
> 06:37:08 T:2860575552  NOTICE: Creating InputStream
> 06:37:08 T:2860575552  NOTICE: Creating Demuxer
> 06:37:08 T:2860575552  NOTICE: Opening video stream: 0 source: 256
> 06:37:08 T:2860575552  NOTICE: Creating video codec with codec id: 2
> 06:37:08 T:2860575552  NOTICE: CDVDVideoCodecFFmpeg::Open() Creating VDPAU(1440x1080, 2)
> 06:37:08 T:2860575552  NOTICE: vdp_device = 0x00000001 vdp_st = 0x00000000
> 06:37:08 T:2860575552  NOTICE: VDPAU Decoder capabilities:
> 06:37:08 T:2860575552  NOTICE: name          level macbs width height
> 06:37:08 T:2860575552  NOTICE: ------------------------------------
> 06:37:08 T:2860575552  NOTICE: MPEG1             0  8192  2048  2048
> 06:37:08 T:2860575552  NOTICE: MPEG2_SIMPLE      3  8192  2048  2048
> 06:37:08 T:2860575552  NOTICE: MPEG2_MAIN        3  8192  2048  2048
> 06:37:08 T:2860575552  NOTICE: H264_MAIN        41  8192  2048  2048
> 06:37:08 T:2860575552  NOTICE: H264_HIGH        41  8192  2048  2048
> 06:37:08 T:2860575552  NOTICE: VC1_SIMPLE        1  8190  2048  2048
> 06:37:08 T:2860575552  NOTICE: VC1_MAIN          2  8190  2048  2048
> 06:37:08 T:2860575552  NOTICE: VC1_ADVANCED      4  8190  2048  2048
> 06:37:08 T:2860575552  NOTICE: MPEG4_PART2_ASP   5  8192  2048  2048
> 06:37:08 T:2860575552  NOTICE: ------------------------------------
> 06:37:08 T:2860575552  NOTICE: Mixer feature: VDP_VIDEO_MIXER_FEATURE_NOISE_REDUCTION
> 06:37:08 T:2860575552  NOTICE: Mixer feature: VDP_VIDEO_MIXER_FEATURE_SHARPNESS
> 06:37:08 T:2860575552  NOTICE: Mixer feature: VDP_VIDEO_MIXER_FEATURE_DEINTERLACE_TEMPORAL
> 06:37:08 T:2860575552  NOTICE: Mixer feature: VDP_VIDEO_MIXER_FEATURE_DEINTERLACE_TEMPORAL_SPATIAL
> 06:37:08 T:2860575552  NOTICE: Mixer feature: VDP_VIDEO_MIXER_FEATURE_INVERSE_TELECINE
> 06:37:08 T:2860575552  NOTICE: Mixer feature: VDP_VIDEO_MIXER_FEATURE_HIGH_QUALITY_SCALING_L1
> 06:37:08 T:2860575552  NOTICE: CDVDVideoCodecFFmpeg::Open() Using codec: MPEG-1/2 video (VDPAU acceleration)
> 06:37:08 T:2860575552  NOTICE: Creating video thread
> 06:37:08 T:2800745280  NOTICE: Thread CDVDPlayerVideo start, auto delete: false
> 06:37:08 T:2800745280  NOTICE: running thread: video_thread
> 06:37:08 T:2860575552  NOTICE: Opening audio stream: 1 source: 256
> 06:37:08 T:2860575552  NOTICE: Finding audio codec for: 86019
> 06:37:08 T:2860575552  NOTICE: Creating audio thread
> 06:37:08 T:2783959872  NOTICE: Thread CDVDPlayerAudio start, auto delete: false
> 06:37:08 T:2783959872  NOTICE: running thread: CDVDPlayerAudio::Process()
> 06:37:08 T:2783959872   ERROR: CDVDPlayerAudio::DecodeFrame - Decode Error. Skipping audio packet
> 06:37:08 T:2783959872  NOTICE: Creating audio device with codec id: 86019, channels: 5, sample rate: 48000, no pass-through
> 06:37:08 T:2800745280  NOTICE:  (VDPAU) screenWidth:1440 vidWidth:1440 surfaceWidth:1440
> 06:37:08 T:2800745280  NOTICE:  (VDPAU) screenHeight:1080 vidHeight:1080 surfaceHeight:1080
> 06:37:08 T:2831436608  NOTICE: Thread Vdpau Output Thread start, auto delete: false
> 06:37:08 T:2831436608  NOTICE: COutput::OnStartup: Output Thread created
> 06:37:08 T:2831436608  NOTICE: VDPAU::COutput::CreateGlxContext - created context
> 06:37:08 T:2831436608  NOTICE: VDPAU::COutput GL interop supported
> 06:37:08 T:2831436608  NOTICE: VDPAU::COutput: vdpau gl interop initialized
> 06:37:08 T:2755636032  NOTICE: Thread Vdpau Mixer Thread start, auto delete: false
> 06:37:08 T:2755636032  NOTICE: CMixer::OnStartup: Output Thread created
> 06:37:08 T:2755636032  NOTICE:  (VDPAU) Creating the video mixer
> 06:37:09 T:2831436608  NOTICE: VDPAU::COutput::InitBufferPool - Output Surface created
> 06:37:09 T:2831436608  NOTICE: Previous line repeats 8 times.
> 06:37:09 T:2831436608  NOTICE: VDPAU::COutput registered output surfaces
> 06:37:09 T:2800745280  NOTICE:  fps: 25.000000, pwidth: 1440, pheight: 1080, dwidth: 1440, dheight: 808
> 06:37:09 T:2800745280  NOTICE: Display resolution DESKTOP : 1920x1080 @ 60.00 - Full Screen (12)
> 06:37:09 T:3011709248  NOTICE: Using GL_TEXTURE_2D
> 06:37:09 T:3011709248  NOTICE: GL: Using VDPAU render method
> 06:37:09 T:3011709248  NOTICE: GL: NPOT texture support detected
> 06:37:09 T:3011709248  NOTICE: GL: Using GL_ARB_pixel_buffer_object
> 06:37:09 T:2800745280 WARNING: CRenderManager::WaitForBuffer - timeout waiting for buffer
> 06:37:14 T:2783959872 WARNING: Previous line repeats 5 times.
> 06:37:14 T:2783959872   ERROR: CDVDPlayerAudio::DecodeFrame - Decode Error. Skipping audio packet
> 06:37:14 T:2860575552  NOTICE: CDVDPlayer::OnExit()
> 06:37:14 T:2860575552  NOTICE: DVDPlayer: eof, waiting for queues to empty
> 06:37:14 T:2860575552  NOTICE: DVDPlayer: closing audio stream
> 06:37:14 T:2860575552  NOTICE: Closing audio stream
> 06:37:14 T:2860575552  NOTICE: CDVDMessageQueue(audio)::WaitUntilEmpty
> 06:37:14 T:2783959872 WARNING: CDVDMessageQueue(audio)::Get - asked for new data packet, with nothing available
> 06:37:14 T:2860575552  NOTICE: Waiting for audio thread to exit
> 06:37:14 T:2783959872  NOTICE: thread end: CDVDPlayerAudio::OnExit()
> 06:37:14 T:2860575552  NOTICE: Closing audio device
> 06:37:14 T:2860575552  NOTICE: Deleting audio codec
> 06:37:14 T:2860575552  NOTICE: DVDPlayer: closing video stream
> 06:37:14 T:2860575552  NOTICE: Closing video stream
> 06:37:14 T:2860575552  NOTICE: CDVDMessageQueue(video)::WaitUntilEmpty
> 06:37:14 T:2860575552  NOTICE: waiting for video thread to exit
> 06:37:14 T:2800745280  NOTICE: thread end: video_thread
> 06:37:14 T:2860575552  NOTICE: deleting video codec
> 06:37:14 T:2860575552  NOTICE: CVDPAU::Release pre-cleanup
> 06:37:14 T:2860575552  NOTICE: CDVDPlayer::OnExit() deleting demuxer
> 06:37:14 T:2860575552  NOTICE: CDVDPlayer::OnExit() deleting input stream
> 06:37:14 T:3011709248  NOTICE: ----------- no buffer, out: 1, current: 1, display: 0
> 06:37:14 T:2860575552  NOTICE: Thread Background Loader start, auto delete: false
> 06:37:14 T:3011709248  NOTICE: CDVDPlayer::CloseFile()
> 06:37:14 T:3011709248 WARNING: CDVDMessageQueue(player)::Put MSGQ_NOT_INITIALIZED
> 06:37:14 T:3011709248  NOTICE: DVDPlayer: waiting for threads to exit
> 06:37:14 T:3011709248  NOTICE: DVDPlayer: finished waiting
> 06:37:14 T:3011709248  NOTICE:  (VDPAU) Close
> 06:37:14 T:3011709248  NOTICE:  (VDPAU) FiniVDPAUOutput
> 06:37:14 T:2755636032  NOTICE: CMixer::OnExit: Output Thread terminated
> 06:37:14 T:2831436608  NOTICE: VDPAU::COutput: vdpau gl interop finished
> 06:37:14 T:2831436608  NOTICE: COutput::OnExit: Output Thread terminated