I reproduced this bugs on 3 computer under Windows 7 64 (pro and ultimate):

In Blender 2.63, i made a video sequence as explained here http://www.blenderguru.com/videos/create-a-sizzling-title-intro , at 41 min 32sec.
My render / encoding params were Mpeg file format + DVD presets with MP3 / 256 kbits.
When i tried to render it, i obtained : Error initializing audio stream.
I saved my scene. And reopened it in 2.63, all my encoding params were saved.

I opened this scene in blender 2.57b.
In the render/encoding section, the file format is PNG while i saved it in MPEG.
I modified the encoding params with Mpeg file format + DVD presets with MP3 / 256 kbits.
I rendered my scene without audio stream error.
The video sequence can be read in VLC.
I save my scene.

I reopend it in blender 2.63 and the rendering work without audio stream error.
I saved the scene in 2.63 on more time.

I reopened it in 2.57 version : the encoding section stayed the same with the good MPEG params.

I noticed differences in scene file size:
- the initial blender 2.63 scene : 621 Kbytes
- reopened and saved in 2.57 : 548 Kbytes
- final from 2.57 reopened and saved in 2.63 : 611 Kbytes.