Thanks for bumping this thread. I meant to get back to you on it, but I forgot.
This is almost certainly that you are using a "bad" DirectShow filter to play back the files. I've seen similar behavior before on my own system with my H264 TS files recorded by my DVR application. It is usually a simple matter of switching the active filters to a better set to fix it up.
Do me a favor... Play one of the "broken" files back, and while it is playing right click on the playback window and choose DirectShow filters -> Copy graph info to clipboard. Then come back here to the forum and paste the contents of the clipboard into a new forum post, like this:
Filter Graph Info:
Filter 'JRiver Audio Renderer'
CLSID: {A4002F8E-510F-442C-8AD3-F9C7B23FB394}
Host:
Input Pin 'In'
Connected to pin 'Out' of filter 'ffdshow Audio Decoder'
Major type MEDIATYPE_Audio Sub type MEDIASUBTYPE_PCM, Format type FORMAT_WaveFormatEx
Filter 'Enhanced Video Renderer'
CLSID: {FA10746C-9B63-4B6C-BC49-FC300EA5F256}
Host: c:\windows\system32\evr.dll
Input Pin 'EVR Input0'
Connected to pin 'Output' of filter 'CoreAVC Video Decoder'
Major type MEDIATYPE_Video Sub type MEDIASUBTYPE_NV12, Format type FORMAT_VideoInfo2
Input Pin 'EVR Input1'
Filter 'ffdshow Audio Decoder'
CLSID: {0F40E1E5-4F79-4988-B1A9-CC98794E6B55}
Host: c:\program files\combined community codec pack\filters\ffdshow\ffdshow.ax
Output Pin 'Out'
Connected to pin 'In' of filter 'JRiver Audio Renderer'
Major type MEDIATYPE_Audio Sub type MEDIASUBTYPE_PCM, Format type FORMAT_WaveFormatEx
Input Pin 'In'
Connected to pin 'Output' of filter 'JRiver Media Proxy Audio'
Major type MEDIATYPE_Audio Sub type Unknown GUID Name: {000000FF-0000-0010-8000-00AA00389B71}, Format type FORMAT_WaveFormatEx
Filter 'CoreAVC Video Decoder'
CLSID: {09571A4B-F1FE-4C60-9760-DE6D310C7C31}
Host: c:\program files\corecodec\coreavc professional edition\coreavcdecoder.ax
Input Pin 'Input'
Connected to pin 'Output' of filter 'JRiver Media Proxy Video'
Major type MEDIATYPE_Video Sub type Unknown GUID Name: {31637661-0000-0010-8000-00AA00389B71}, Format type FORMAT_MPEG2_VIDEO
Output Pin 'Output'
Connected to pin 'EVR Input0' of filter 'Enhanced Video Renderer'
Major type MEDIATYPE_Video Sub type MEDIASUBTYPE_NV12, Format type FORMAT_VideoInfo2
Filter 'JRiver Media Proxy Audio'
CLSID: {A4207487-E7D8-406B-9882-B66370DE2492}
Host:
Input Pin 'Input'
Connected to pin 'Apple Sound Media Handler' of filter 'MP4 Source'
Major type MEDIATYPE_Audio Sub type Unknown GUID Name: {000000FF-0000-0010-8000-00AA00389B71}, Format type FORMAT_WaveFormatEx
Output Pin 'Output'
Connected to pin 'In' of filter 'ffdshow Audio Decoder'
Major type MEDIATYPE_Audio Sub type Unknown GUID Name: {000000FF-0000-0010-8000-00AA00389B71}, Format type FORMAT_WaveFormatEx
Filter 'JRiver Media Proxy Video'
CLSID: {A4207487-E7D8-406B-9882-B66370DE2492}
Host:
Input Pin 'Input'
Connected to pin 'Apple Video Media Handler' of filter 'MP4 Source'
Major type MEDIATYPE_Video Sub type Unknown GUID Name: {31637661-0000-0010-8000-00AA00389B71}, Format type FORMAT_MPEG2_VIDEO
Output Pin 'Output'
Connected to pin 'Input' of filter 'CoreAVC Video Decoder'
Major type MEDIATYPE_Video Sub type Unknown GUID Name: {31637661-0000-0010-8000-00AA00389B71}, Format type FORMAT_MPEG2_VIDEO
Filter 'MP4 Source'
CLSID: {3CCC052E-BDEE-408A-BEA7-90914EF2964B}
Host: c:\program files\j river\media center 15\plugins\mp4splitter.ax
Output Pin 'Apple Video Media Handler'
Connected to pin 'Input' of filter 'JRiver Media Proxy Video'
Major type MEDIATYPE_Video Sub type Unknown GUID Name: {31637661-0000-0010-8000-00AA00389B71}, Format type FORMAT_MPEG2_VIDEO
Output Pin 'Apple Sound Media Handler'
Connected to pin 'Input' of filter 'JRiver Media Proxy Audio'
Major type MEDIATYPE_Audio Sub type Unknown GUID Name: {000000FF-0000-0010-8000-00AA00389B71}, Format type FORMAT_WaveFormatEx
PLEASE NOTE: After you paste this code into the forum post, please select the text you just pasted and then click the # button in the forum's post editor. This will wrap the text in a CODE block tag, which puts it in the gray box like mine above, and makes it much easier for us to read.