Files and Folders Missing

I have a Windows Home Server 2011 running with Stablebit Drive Pool. The only files and folders I'm using in Serviio are on the drive K: "the drive pool drive, which is being shared" This use to work fine and I was able to see all the files on my other computers and 2 Sony SMP-N200. But now we are only seeing 51 of the 750 files.

Here's a sample off 2 outputs - Thor works fine and Red does not:

This one works and is seen.

C:\Program Files\Serviio\lib>ffmpeg.exe -i "K:\thor.mkv"
ffmpeg version N-54096-ge41bf19 Copyright (c) 2000-2013 the FFmpeg developers
built on Jun 18 2013 10:49:28 with gcc 4.7.2 (GCC)
configuration: --enable-static --disable-shared --disable-ffplay --disable-ffs
erver --enable-memalign-hack --enable-libmp3lame --enable-libass --enable-librtm
p --enable-fontconfig --enable-libfreetype --enable-zlib --enable-libx264 --extr
a-libs='-lrtmp -lpolarssl -lws2_32 -lwinmm -lexpat -lfreetype -lfribidi -lz' --a
rch=x86 --enable-runtime-cpudetect --enable-pthreads --target-os=mingw32 --cross
-prefix=i686-w64-mingw32- --enable-gpl --pkg-config=pkg-config
libavutil 52. 37.101 / 52. 37.101
libavcodec 55. 16.100 / 55. 16.100
libavformat 55. 9.100 / 55. 9.100
libavdevice 55. 2.100 / 55. 2.100
libavfilter 3. 77.101 / 3. 77.101
libswscale 2. 3.100 / 2. 3.100
libswresample 0. 17.102 / 0. 17.102
libpostproc 52. 3.100 / 52. 3.100
Input #0, matroska,webm, from 'K:\thor.mkv':
Metadata:
creation_time : 2011-08-25 21:59:34
Duration: 01:54:50.67, start: 0.000000, bitrate: 9528 kb/s
Stream #0:0(eng): Video: h264 (High), yuv420p, 1920x816, SAR 1:1 DAR 40:17,
23.98 fps, 23.98 tbr, 1k tbn, 47.95 tbc
Stream #0:1(eng): Audio: dts (DTS), 48000 Hz, 5.1(side), fltp, 1536 kb/s (de
fault)
Metadata:
title : english
Stream #0:2(eng): Subtitle: subrip
Metadata:
title : english
At least one output file must be specified

This one does not work

C:\Program Files\Serviio\lib>ffmpeg.exe -i "K:\red.mkv" |clip
ffmpeg version N-54096-ge41bf19 Copyright (c) 2000-2013 the FFmpeg developers
built on Jun 18 2013 10:49:28 with gcc 4.7.2 (GCC)
configuration: --enable-static --disable-shared --disable-ffplay --disable-ffs
erver --enable-memalign-hack --enable-libmp3lame --enable-libass --enable-librtm
p --enable-fontconfig --enable-libfreetype --enable-zlib --enable-libx264 --extr
a-libs='-lrtmp -lpolarssl -lws2_32 -lwinmm -lexpat -lfreetype -lfribidi -lz' --a
rch=x86 --enable-runtime-cpudetect --enable-pthreads --target-os=mingw32 --cross
-prefix=i686-w64-mingw32- --enable-gpl --pkg-config=pkg-config
libavutil 52. 37.101 / 52. 37.101
libavcodec 55. 16.100 / 55. 16.100
libavformat 55. 9.100 / 55. 9.100
libavdevice 55. 2.100 / 55. 2.100
libavfilter 3. 77.101 / 3. 77.101
libswscale 2. 3.100 / 2. 3.100
libswresample 0. 17.102 / 0. 17.102
libpostproc 52. 3.100 / 52. 3.100
Input #0, matroska,webm, from 'K:\red.mkv':
Metadata:
creation_time : 2011-01-17 18:07:54
Duration: 01:51:09.65, start: 0.000000, bitrate: 10226 kb/s
Stream #0:0(eng): Video: h264 (High), yuv420p, 1920x800, SAR 1:1 DAR 12:5, 2
3.98 fps, 23.98 tbr, 1k tbn, 47.95 tbc (default)
Stream #0:1(eng): Subtitle: subrip (default)
Stream #0:2(fre): Audio: ac3, 48000 Hz, 5.1(side), fltp, 640 kb/s (default)
(forced)
Metadata:
title : Ac3 640 Kbps
Stream #0:3: Subtitle: subrip
Stream #0:4(eng): Audio: dts (DTS), 48000 Hz, 5.1(side), fltp, 1536 kb/s
Metadata:
title : DTS 1509 Kbps

Here is the output from the Serviio log for Red:
2013-12-01 01:28:52,993 WARN [LibraryManager] Skipping processing metadata for an unsupported file (Red.mkv). Message: Unknown video file type.

[zip]

Are you running 1.3.1?

Also check the access rights to the 2 files and if they are the same.