Ipod classic 120g not showing captions

I am using 6th gen ipod classic (thinner version.) My firmware is 2.0.1.
I am having problems that my captions (subtitles) aren't showing up in videos. They show up in iTunes but when I sync them, nothing goes on.
I enabled captions in iPod settings but still no luck.
I tried both Handbrake and iSubtitle for creating captioned video, both of them work in iTunes but not working in iPod. (and yes, I have tried switching between captions and subtitle options.

I have the same problem on my iPod Classic (3rd Gen firmware 2.0.4) since last system upgrade. Before it my iPod was able to play movies and show subtitles.
I have many movies converted for my iPod with soft subtitles, I've done it with Handbrake and in the past with another commercial program: on my iPhone 3GS (last firmware) subtitles work, on my iPod Nano (fatty) subtitles work on my iPod Classic subtitles worked!
The strange thing is that also iTunes has a strange behaviour about subtitles now. As matter of fact, now I can't enable (or disable) the subtitles (using menu or button on floating interface) while if I open the movie using Quicktime X or Quicktime 7 I can. It's very strange and annoying.
I already tried to restore firmware, to re-install iTunes, to repair authorizations but nothing, it's always the same.
I try to find clue googling around and I read about other users with same issues and in a forum someone said "Starting in 10.6.7, iTunes uses a AVFoundation to play movies instead of QuickTime, so there are some new bugs."
Maybe he's right but I really don't understand why and how this AVFoundation can affect on my iPod Classic.
Please, is there some Apple Guru that can explain us, how we can solve this issue?

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