ps3muxer uses tsmuxer for transcoding mkv to m2ts and use ffmpeg for converting dts to ac3.
But for audio conversion I suggest eac3to which is better in handling HD audios.
Just see the post before this one.
For mov files--(not sure what's audio codec is)
load to mkvmerge gui-->convert to mkv-->see the post before-->load to hd stream extractor-->convert audio to AC3/dolby digital-->now mux using tsmuxer.
First try to load straight to tsmuxer..check if audio is coming or it's eliminating the audio.
I too notice audio quality bit deteriorate by ps3 muxer.
Regarding codec of mov files...
Video
ID/String : 1
Format : AVC
Format/Info : Advanced Video Codec
Format_Profile :
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Format_Settings_CABAC/String : No
Format_Settings_RefFrames/String : 1 frame
Format_Settings_GOP : M=1, N=15
CodecID : avc1
CodecID/Info : Advanced Video Coding
Duration/String : 1mn 10s
BitRate/String : 23.4 Mbps
Width/String : 1 280 pixels
Height/String : 720 pixels
DisplayAspectRatio/String : 16:9
FrameRate_Mode/String : Constant
FrameRate/String : 29.970 fps
ColorSpace : YUV
ChromaSubsampling : 4:2:0
BitDepth/String : 8 bits
ScanType/String : Progressive
Bits-(Pixel*Frame) : 0.847
StreamSize/String : 197 MiB (97%)
Language/String : English
Encoded_Date : UTC 2012-09-14 13:49:37
Tagged_Date : UTC 2012-09-14 13:49:37
Color primaries : BT.709
Transfer characteristics : BT.709
Matrix coefficients : BT.601
Audio
ID/String : 2
Format : PCM
Format_Settings_Endianness : Little
Format_Settings_Sign : Signed
CodecID : sowt
Duration/String : 1mn 10s
BitRate_Mode/String : Constant
BitRate/String : 768 Kbps
Channel(s)/String : 1 channel
ChannelPositions : Front: C
SamplingRate/String : 48.0 KHz
BitDepth/String : 16 bits
StreamSize/String : 6.45 MiB (3%)
Language/String : English
Encoded_Date : UTC 2012-09-14 13:49:37
Tagged_Date : UTC 2012-09-14 13:49:37