Not transcoded but altered - Why?

Question

Hi everyone, I'm having some big problems trying to build a project meant to be deployable to a media player.
I won't pretend to claim I understand the standards involved that well but I don't think I have crossed the boundaries (at least not
too far).
The aim is to take a considerable amount of HD footage (upto 20 hours) into a navigated video. By that I mean the footage has
various sections which the viewer should be able to randomly navigate to but otherwise the video plays as a continuous stream. My
idea was to use blu-ray menus but not with a blu-ray disc. A few media players are blu-ray menu compatible and are able to play from
blu-ray format folders or ISO's where the navigation works as if it were a blu-ray disc in a blu-ray player.
The source footage is from an AVCHD camera (Canon).
To do all of this I am using Encore 5.1 (as per CS5.5). Encore now allows AVCHD video to be passed through without transcoding.
All of this seems to work except Encore is doing something I don't quite understand which is ruining the result.
Encore will of course have to render the menus etc. but it should just pass through the orginal AVCHD footage. But what seems to be
happening is that the footage is altered. The video seems to be untouched visually but it's attibutes don't make sense and the audio
is redone and the container timing is totally wrong.
You can see what I mean if you look at the exports from MediaInfo pasted below. I have tried to change quality presets and so on,
but it makes no difference. Maybe I am doing this all wrong and need some pointers if someone knows how to do this.
The first export is from a scene as it has come from the camera. The second is the same clip after Encore has created the blu-ray
folders. As far as I know the camera AVCHD clip should be blu-ray H.264 compliant and in theory transfer unaltered.
For the container timing, notice that out of the camera it is 06:12. But out of Encore it has changed to 07:39. If you look at the
video both are still at 06:12 but the audio out of Encore is now 07:39. Near the end of the clip, the video freezes but the audio
runs on, so it seems to have lost sync. For some reason, while the max bit rate for the video is the same the average rate is now
only 12.6 whereas the orginal was 15.5. The bits/px and stream size have also dropped but no render took place (or my computer has
suddenly gone into turbo mode) which sounds like bits were just dropped out. Also, for the audio, the orginal was Dolby AC-3 but at
256Kbps. For some reason it is longer but the bit rate has dropped to only 192Kbps.
This is happening to every single clip.
What have I missed here?
-Richard
**********CAMERA*********
General
ID                               : 0 (0x0)
Complete name                    : D:\Video\M2009\M2009_Scenes\0010_20091005102604.mts
Format                           : BDAV
Format/Info                      : Blu-ray Video
File size                        : 730 MiB
Duration                         : 6mn 12s
Overall bit rate mode            : Variable
Overall bit rate                 : 16.4 Mbps
Maximum Overall bit rate         : 18.0 Mbps
Video
ID                               : 4113 (0x1011)
Menu ID                          : 1 (0x1)
Format                           : AVC
Format/Info                      : Advanced Video Codec
Format profile                   : [email protected]
Format settings, CABAC           : Yes
Format settings, ReFrames        : 2 frames
Format settings, GOP             : M=3, N=12
Codec ID                         : 27
Duration                         : 6mn 12s
Bit rate mode                    : Variable
Bit rate                         : 15.5 Mbps
Maximum bit rate                 : 16.0 Mbps
Width                            : 1 920 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
Bits/(Pixel*Frame)               : 0.299
Stream size                      : 689 MiB (94%)
Audio
ID                               : 4352 (0x1100)
Menu ID                          : 1 (0x1)
Format                           : AC-3
Format/Info                      : Audio Coding 3
Mode extension                   : CM (complete main)
Codec ID                         : 129
Duration                         : 6mn 12s
Bit rate mode                    : Constant
Bit rate                         : 256 Kbps
Channel(s)                       : 2 channels
Channel positions                : Front: L R
Sampling rate                    : 48.0 KHz
Bit depth                        : 16 bits
Compression mode                 : Lossy
Delay relative to video          : -80ms
Stream size                      : 11.4 MiB (2%)
********ENCORE*************
General
ID                               : 0 (0x0)
Complete name                    : D:\Video\M2009\Projects\Media\M2009\BDMV\STREAM\00014.m2ts
Format                           : BDAV
Format/Info                      : Blu-ray Video
File size                        : 732 MiB
Duration                         : 7mn 39s
Overall bit rate mode            : Variable
Overall bit rate                 : 13.4 Mbps
Maximum Overall bit rate         : 48.0 Mbps
Video
ID                               : 4113 (0x1011)
Menu ID                          : 1 (0x1)
Format                           : AVC
Format/Info                      : Advanced Video Codec
Format profile                   : [email protected]
Format settings, CABAC           : Yes
Format settings, ReFrames        : 2 frames
Format settings, GOP             : M=3, N=12
Codec ID                         : 27
Duration                         : 6mn 12s
Bit rate mode                    : Variable
Bit rate                         : 12.6 Mbps
Maximum bit rate                 : 16.0 Mbps
Width                            : 1 920 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
Bits/(Pixel*Frame)               : 0.244
Stream size                      : 561 MiB (77%)
Audio
ID                               : 4352 (0x1100)
Menu ID                          : 1 (0x1)
Format                           : AC-3
Format/Info                      : Audio Coding 3
Mode extension                   : CM (complete main)
Codec ID                         : 129
Duration                         : 7mn 39s
Bit rate mode                    : Constant
Bit rate                         : 192 Kbps
Channel(s)                       : 2 channels
Channel positions                : Front: L R
Sampling rate                    : 48.0 KHz
Bit depth                        : 16 bits
Compression mode                 : Lossy
Delay relative to video          : -80ms
Stream size                      : 10.5 MiB (1%)

Answer 1

The timelines you requested are attached.
The one labeled leader is a first play.
The one labeled mainline is the one with back to back video.
With reference to Stan's suggestion this does indeed seem to fix the problem.
The videos are still altered but only by a few bytes example original: 107106, after encore: 107232. The timing is also changed by only by a few milliseconds.For this short example you can't tell the difference.
The audio is also back to 256Kbps AC-3 which is what the source is which is great!
I was not expecting this to happen. It makes things a bit more difficult since I would need to use volumes of timelines or a better alternative is to join the clips before import. Fortunately TXmuxeR does a good job of this but I would have to write some scripts to generate the muxing config - it's too hard to do manually for more than a handful of clips but not too hard to do with a bit of Perl or Python.
However, I was heading down this path anyway since my final project could have hundreds of clips and the more you put the longer En takes to startup so I'm not too fussed about doing the scripting. I was perhaps hoping En would handle this for me - Obviously not.
I am still confused though. Firstly why is En still touching the clips at all? Second, it seems strange that a timeline is so restrictive in what can be put into it. Are you saying not to combine anything into a timeline or just don't combine clips or don't combine muxed clips?
Thanks for you comments, it's given me some new directions to try.
- Richard