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I got around this problem by switching from mplayer to gmplayer. I don't know what the difference is, or why the php class that handles the video duration functions seems to handle it differently.
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Yeah, that works fine too. I cannot reproduce the error on the commandline as any user.

What's weird is the format of the error:

sh: /usr/bin/mplayer: Permission Denied

I only see it in the...

Here's what I get doing that as the nobody user:

# sudo -u nobody ls -l /usr/bin | grep mplayer
-rwxr-xr-x 1 root root 8207616 Dec 4 2008 gmplayer
-rwxr-xr-x 1 root root 7741080 Dec 4 ...

I'm not sure where the problem is. This is what I'm seeing in the conversion report:

Video id: 12
Video Output File Name :...