Audio messed up in BD

I was trying to build a BD using two clips made with PPro in H.264 Bluray format. After creating chapters and menus, the preview looks fine and the audio was in sync. However, once built onto the BD-R, even the navigation is still OK, the audio is gone except for the first chapter where the audio was apparently the one from another chapter later. I have tried to use several different menus later but the results were the same. Strange enough, I made a BD only two weeks ago using the same approach and the disk was perfect.
Any idea what happened?

Bingo! Stan, you were right on the money!!
Thank you so much. I have spent the whole night yesterday trying to figure out what has gone wrong. Putting clips on different timelines is OK, but it will be harder to leverage the automatic chapter index creation on submenus.

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---- System ----
System: Linux 2.6.31-ARCH x86_64
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Set SSE3 simd processor
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Audio messed up in BD

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