Alright so I got it all working, all MKV's now play with sound! I changed it so when they transcode, they change the audio codec to something PS3 friendly. I know it's probably over kill to change the audio codec for all MKV's but at least they all now work as expected!... I also added to the command to include any subtitle files if they exist. Here is my new exec command:
exec: ffmpeg -threads 2 -i $infile -vcodec mpeg2video -sameq -scodec copy -acodec ac3 -ab 384k -f vob -copyts -y $outfile
-scodec copy option allows it to copy across subtitles included in the MKV. -acodec ac3 -ab 384k is changing the audio codec and bit-rate, i found AC3 worked best and that bit-rate I just randomly selected, it can be increased/decreased as required.
I hope this helps somebody else out!
* Also I changed it to be an asynchronous transcode. I just found this to worked better.