So from what i can see this script demuxes a mkv and remuxes it to mp4 with aac audio, the probabolity is that your mkv does not have a PS3 compatible h264 stream in it....
I'd be running your video through a speciffic PS3 encoding script then comparing the streams...
I also notice that you have modded the script, try with a unmodded script and install the required packages, authors usually choose to use certain packages for a reason!
But the next question is why are you remuxing mkv's why don't you just recode your original disc?
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