Actually, good catch. There is indeed a bug for both window and linux, in vlc2.x and probably also in previous versions.
The reason is that the "main input manager" is initialized with input set to NULL.
On qt4, this singleton is created when the qt4 "main interface" is created. So chances are that no input is launched yet. Still the design makes it possible for an input to be started before the interface is fully initialized (the case when a file is provided at the command line is such a case if I recall correctly). I would say the bug exists with qt4 but it is hardly ever noticed.
On skins2, this singleton is created on first use, i.e the first time the user right clicks to access the popupmenu. And indeed, the first playback doesn't display these video/audio/subttiles menus, since the input was launched prior to the singleton creation. As soon as a second input is started, the bug disappears, since the singleton then lives till the end of the vlc instance.
Basically you're saying to avoid this bug I have to open VLC, then open the video file using VLC instead of just double clicking on the file itself to open VLC? I've just tested this, and opening files by this method does fix my problem. Will this bug be fixed in future released of VLC? I can verify that it was not present (for me at least) in VLC 1.1.11 on Windows 7.
Thank you very much for the help.