Audio silent on some chapters after build?

I've looked through the forum and can't find an answer to this.
I have authored and built a dual layer DVD, but past a certain point the audio stops playing on all tracks when playing a burnt disk in a DVD player, and in apple dvd player when playing the dvd from a video_ts folder. All the audio plays correctly in the simulator.
at the moment all the video is one track (over four hours), using multiple stories to play different sections (reason I've dont it this way is I want a playall that allows the user to step through every thing on the disk chapter by chapter)
all audio is encoded the same, ac3 48 khz, 192 VBR, 16 bit (default for audio). However the video bitrate average and max is varying for each chapter (its lots of video clips layed into one track).
any ideas? all I can think of is re encoding all the audio again on one computer or breaking the project up into multiple tracks and trying to use scripting to provide the play all functionality I want.
forgot to add, I know about compatibility problems with video bit rate too high. nothing has a higher bitrate than the "dvd best quality 90 minutes" standard preset (avg 6.2 max 7.7), most of the video has the bitrate lowered to 5.0 avg or 3.7mps avg.

The audio needs to be that same rate, video clips do not have to be the same rate
If you are able to make tracks shorter than 3 hours 15 minutes it seems to help on the Apple DVD Player side of things (no MPEG blocking/corruption/audio dropouts), as to why it is not working properly on a DVD Player (standalone) I am not sure, perhaps the bug carried over to the builds.
Couple of things to check - what type of media did you use? Also check the audio to make sure things were not panned too much one way or the other and some players, such as Sony's, have faux "surround sound" which does strange things to audio, including drop outs (same for cycling through certain audio settings on players, some of them behave poorly.)
Lastly (and it is VERY strange) I have seen bad cables cause issues where audio drop out (and/or MPEG corruption) on certain parts of DVDs while other DVDs did not have the issue and changing the cables, resetting connections helped.

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