I reconverted many 20min videos with H.264 x.264 / AAC and it went all good, but then with the same codecs I converted 2 movies that were 1h40min and the video track became 50min long while the audio track was still 1h40min.
The images look accelerated, I guess some frames have been omitted but I don't understand what happened, I did not change the video parameters after opening the movie in ffmpegX
Attached is the preset I used for the first movie.
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Try decoding with QT and see if this problem goes away. I've not encountered this before, but apparently others have. Generally speaking, QT seems to handle timing a bit better, so if your transcoding options allow its use, it's probably a good choice. It's worth a try, in any case.