i really dont think that it's the program that's causing the off-synching of the audio. it is more of the proper settings of the codes. phones have limited memory and speed, that it takes time to read video data causing it to off synch with the audio. had experienced this too before, but solved this by lowering the converted quality so that the phone can cope up with the audio/video.
note that if you try to play the (off-synch) converted file in a pc, you will not notice the off-synch part