MKV remuxing without transcoding

I have a Synology NAS running Serviio, the renderer is a Sharp Aquos. I can usually watch movies from the NAS fairly well. When playing MKV files, I see that my serviio is running ffmpeg to transcode these mkv files to stf's.. Because of the lack of CPU power on the Synology, it takes several hours and sometimes days to convert these, which makes it nearly useless. After reading through this forum and synology forums, I have tried to run ffmpeg and once the stf file is created, I rename it to mpeg and use it. This is to avoid the transcoding on the fly everytime. However, the mpeg does not have audio, that makes it useless. I have read in some of the forums that you dont have to transcode the mkv files, just remuxing them would work. Is that right? If so how do I do that?
Secondly, can I have a background task that would convert these MKVs and store them in mpeg or some other format (without a lot of loss in quality) so that I dont have to transcode these files on the fly and just use them? If so how do can I do that. The following is the output of ffmpeg of the file that I was complaining to not have any audio.
DiskStation> ffmpeg -i kalvarey-temp-124-MPEG2PS.stf
ffmpeg version UNKNOWN, Copyright (c) 2000-2011 the FFmpeg developers
built on Sep 4 2011 02:28:29 with gcc 4.2.1
configuration: --arch=arm --target-os=linux --cross-prefix=/usr/local/arm-none-linux-gnueabi/bin/arm-none-linux-gnueabi- --enable-cross-compile --enable-optimizations --disable-yasm --disable-altivec --enable-pic --enable-shared --disable-static --disable-swscale-alpha --disable-ffserver --disable-ffplay --enable-libmp3lame
libavutil 50. 40. 1 / 50. 40. 1
libavcodec 52.120. 0 / 52.120. 0
libavformat 52.108. 0 / 52.108. 0
libavdevice 52. 4. 0 / 52. 4. 0
libavfilter 1. 77. 0 / 1. 77. 0
libswscale 0. 14. 0 / 0. 14. 0
Input #0, mpeg, from 'kalvarey-temp-124-MPEG2PS.stf':
Duration: 00:02:52.29, start: 1.000000, bitrate: 23193 kb/s
Stream #0.0[0x1e0]: Video: mpeg2video (Main), yuv420p, 1920x816 [PAR 1:1 DAR 40:17], 104857 kb/s, 23.98 fps, 23.98 tbr, 90k tbn, 47.95 tbc
At least one output file must be specified
DiskStation>
Thanks
Senthil
Secondly, can I have a background task that would convert these MKVs and store them in mpeg or some other format (without a lot of loss in quality) so that I dont have to transcode these files on the fly and just use them? If so how do can I do that. The following is the output of ffmpeg of the file that I was complaining to not have any audio.
DiskStation> ffmpeg -i kalvarey-temp-124-MPEG2PS.stf
ffmpeg version UNKNOWN, Copyright (c) 2000-2011 the FFmpeg developers
built on Sep 4 2011 02:28:29 with gcc 4.2.1
configuration: --arch=arm --target-os=linux --cross-prefix=/usr/local/arm-none-linux-gnueabi/bin/arm-none-linux-gnueabi- --enable-cross-compile --enable-optimizations --disable-yasm --disable-altivec --enable-pic --enable-shared --disable-static --disable-swscale-alpha --disable-ffserver --disable-ffplay --enable-libmp3lame
libavutil 50. 40. 1 / 50. 40. 1
libavcodec 52.120. 0 / 52.120. 0
libavformat 52.108. 0 / 52.108. 0
libavdevice 52. 4. 0 / 52. 4. 0
libavfilter 1. 77. 0 / 1. 77. 0
libswscale 0. 14. 0 / 0. 14. 0
Input #0, mpeg, from 'kalvarey-temp-124-MPEG2PS.stf':
Duration: 00:02:52.29, start: 1.000000, bitrate: 23193 kb/s
Stream #0.0[0x1e0]: Video: mpeg2video (Main), yuv420p, 1920x816 [PAR 1:1 DAR 40:17], 104857 kb/s, 23.98 fps, 23.98 tbr, 90k tbn, 47.95 tbc
At least one output file must be specified
DiskStation>
Thanks
Senthil