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I have even more information for you.
I am a computer programmer and I could not sit still anymore, so I started looking at mencoder.exe to see if it's the link in the chain that's causing the trouble I have.
I noticed that CloneDVDmobile passes the video and audio data to mencoder through the stanrard-in (stdin). So I created a VOB file using the VOB passthgourh method, end I've encoded it with mencoder to MPEG4, and I was glad to see that it was encoded correctly without cutting off anything at the beginning.
So I think the developers in your team should look at the data they pass to mencoder via the stdin, because they're truncating something at the beginning.
Well, thanks for testing that. But, nope, CloneDVD mobile doesn't truncate anything.
Actually when you generate a VOB (passthrough) file, CloneDVD mobile simply sends the exact same data it would pipe into mencoder into a file. That's the only difference. So when you're looking at the VOB file, you see precisely the same data that mencoder receives.
So it's a bug in the way mencoder handles input from stdin. My guess is that you'll get the same result if you stream the VOB file into mencoder from the cmdline.
I'm aware of this "problem" - honestly, I find it difficult to see it as such, after all it is hard to find source material, where cutting off the first second results in anything more than 2 seconds of blackness instead of 3. And even in the other cases, like when I'm transcoding a specific chapter, I'd hardly call it a show stopper to miss a second from the beginning.
Nevertheless, I'll keep trying, but it is extremely hard to induce changes in mencoder. The developers have their own priorities.