ffmpeg concat output not playing in windows media player

I have a series of short (<3sec) mp4 videos (some with audio, some with no audio) that play fine in all clients. 15 fps, AAC audio. When I use ffmpeg concat, the resulting file plays fine in vlc, however in winmedia it ignores any silence in the audio track. In quicktime it plays all the video, only plays the first audio. I feel it has something to do with syncing video and audio but am new with ffmpeg. If I take the output and recode it with handbrake, it builds a file that works.

exec ("ffmpeg -f concat -i files.txt -c  copy finalvideo.mp4");

and then I do this:

exec ("ffmpeg -i finalvideo.mp4 -c:v copy -c:a libfaac -r 24 output.mp4");

Revised with new outputs after ensuring that both source audios have the same encoding (I think)

Info from New Pause File

/home/fresh/public_html/ffmpeg/output$ ffmpeg -i /home/fresh/public_html/ffmpeg/output/ENP22122.mp4
ffmpeg version N-61053-gab5d46d-syslint Copyright (c) 2000-2014 the FFmpeg developers
built on Mar  3 2014 13:27:18 with gcc 4.4.7 (GCC) 20120313 (Red Hat 4.4.7-4)
configuration: --prefix=/usr/local/cpffmpeg --enable-shared --enable-nonfree --enable-gpl --enable-pthreads --enable-libopencore-amrnb --enable-decoder=liba52 --enable-  libopencore-amrwb --enable-libfaac --enable-libmp3lame --enable-libtheora --enable-  libvorbis --enable-libx264 --enable-libxvid --extra-cflags=-I/usr/local/cpffmpeg/include/ --extra-ldflags=-L/usr/local/cpffmpeg/lib --enable-version3 --extra-version=syslint
libavutil      52. 66.100 / 52. 66.100
libavcodec     55. 52.102 / 55. 52.102
libavformat    55. 33.100 / 55. 33.100
libavdevice    55. 10.100 / 55. 10.100
libavfilter     4.  2.100 /  4.  2.100
libswscale      2.  5.101 /  2.  5.101
libswresample   0. 18.100 /  0. 18.100
libpostproc    52.  3.100 / 52.  3.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/home/fresh/public_html/ffmpeg/output/ENP22122.mp4':
Metadata:
major_brand     : isom
minor_version   : 512
compatible_brands: isomiso2avc1mp41
encoder         : Lavf55.33.100
Duration: 00:00:04.07, start: 0.000000, bitrate: 63 kb/s
Stream #0:0(und): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 480x360 [SAR 1:1   DAR 4:3], 5 kb/s, 15 fps, 15 tbr, 15360 tbn, 30 tbc (default)
Metadata:
  handler_name    : VideoHandler
Stream #0:1(und): Audio: mp3 (mp4a / 0x6134706D), 44100 Hz, mono, s16p, 96 kb/s (default)
Metadata:
  handler_name    : SoundHandler

Info from new Audio File

/home/fresh/public_html/ffmpeg/output$ ffmpeg -i /home/fresh/public_html/ffmpeg/output/ENT22122.mp4
ffmpeg version N-61053-gab5d46d-syslint Copyright (c) 2000-2014 the FFmpeg developers
built on Mar  3 2014 13:27:18 with gcc 4.4.7 (GCC) 20120313 (Red Hat 4.4.7-4)
configuration: --prefix=/usr/local/cpffmpeg --enable-shared --enable-nonfree --enable-gpl --enable-pthreads --enable-libopencore-amrnb --enable-decoder=liba52 --enable-  libopencore-amrwb --enable-libfaac --enable-libmp3lame --enable-libtheora --enable-libvorbis --enable-libx264 --enable-libxvid --extra-cflags=-I/usr/local/cpffmpeg/include/ --extra-ldflags=-L/usr/local/cpffmpeg/lib --enable-version3 --extra-version=syslint
libavutil      52. 66.100 / 52. 66.100
libavcodec     55. 52.102 / 55. 52.102
libavformat    55. 33.100 / 55. 33.100
libavdevice    55. 10.100 / 55. 10.100
libavfilter     4.  2.100 /  4.  2.100
libswscale      2.  5.101 /  2.  5.101
libswresample   0. 18.100 /  0. 18.100
libpostproc    52.  3.100 / 52.  3.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/home/fresh/public_html/ffmpeg/output/ENT22122.mp4':
Metadata:
major_brand     : isom
minor_version   : 512
compatible_brands: isomiso2avc1mp41
encoder         : Lavf55.33.100
Duration: 00:00:03.07, start: 0.000000, bitrate: 56 kb/s
Stream #0:0(und): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 480x360 [SAR 1:1 DAR 4:3], 6 kb/s, 15 fps, 15 tbr, 15360 tbn, 30 tbc (default)
Metadata:
  handler_name    : VideoHandler
Stream #0:1(und): Audio: mp3 (mp4a / 0x6134706D), 44100 Hz, mono, s16p, 96 kb/s (default)
Metadata:
  handler_name    : SoundHandler

Output from concat command

/home/fresh/public_html/ffmpeg/output$ ffmpeg -f concat -i /home/fresh/public_html   /ffmpeg/filesnotime.txt -c  copy /home/fresh/public_html/ffmpeg/finalvideo.mp4
ffmpeg version N-61053-gab5d46d-syslint Copyright (c) 2000-2014 the FFmpeg developers
built on Mar  3 2014 13:27:18 with gcc 4.4.7 (GCC) 20120313 (Red Hat 4.4.7-4)
configuration: --prefix=/usr/local/cpffmpeg --enable-shared --enable-nonfree --enable-gpl --enable-pthreads --enable-libopencore-amrnb --enable-decoder=liba52 --enable-libopencore-amrwb --enable-libfaac --enable-libmp3lame --enable-libtheora --enable-libvorbis --enable-libx264 --enable-libxvid --extra-cflags=-I/usr/local/cpffmpeg/include/ --extra-ldflags=-L/usr/local/cpffmpeg/lib --enable-version3 --extra-version=syslint
libavutil      52. 66.100 / 52. 66.100
libavcodec     55. 52.102 / 55. 52.102
libavformat    55. 33.100 / 55. 33.100
libavdevice    55. 10.100 / 55. 10.100
libavfilter     4.  2.100 /  4.  2.100
libswscale      2.  5.101 /  2.  5.101
libswresample   0. 18.100 /  0. 18.100
libpostproc    52.  3.100 / 52.  3.100
[concat @ 0x14a2900] Estimating duration from bitrate, this may be inaccurate
Input #0, concat, from '/home/fresh/public_html/ffmpeg/filesnotime.txt':
Duration: 00:00:00.08, start: 0.000000, bitrate: 102 kb/s
Stream #0:0: Video: h264 (High) (avc1 / 0x31637661), yuv420p, 480x360 [SAR 1:1 DAR 4:3], 6 kb/s, 15 fps, 15 tbr, 15360 tbn, 30 tbc
Stream #0:1: Audio: mp3 (mp4a / 0x6134706D), 44100 Hz, mono, s16p, 96 kb/s
Output #0, mp4, to '/home/fresh/public_html/ffmpeg/finalvideo.mp4':
Metadata:
encoder         : Lavf55.33.100
Stream #0:0: Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 480x360 [SAR 1:1 DAR 4:3], q=2-31, 6 kb/s, 15 fps, 15360 tbn, 15360 tbc
Stream #0:1: Audio: mp3 (i[0][0][0] / 0x0069), 44100 Hz, mono, 96 kb/s
Stream mapping:
Stream #0:0 -> #0:0 (copy)
Stream #0:1 -> #0:1 (copy)

frame=  828 fps=0.0 q=-1.0 Lsize=     392kB time=00:00:55.00 bitrate=  58.4kbits/s    
video:81kB audio:289kB subtitle:0 data:0 global headers:0kB muxing overhead 6.031527%