NOTICE: when i convert videos via terminal and download them from ftp into pc the audio works fine. I use:

if($ext == "avi" && $convert_avi == true)
                {
                    $convert_source = _VIDEOS_DIR_PATH.$new_name;
                    $conv_name = substr(md5($file['name'].rand(1,888)), 2, 10).".mp4";
                    $converted_file  = _VIDEOS_DIR_PATH.$conv_name;
                    $ffmpeg_command = 'ffmpeg -i '.$convert_source.' -acodec libmp3lame -vcodec libx264 -s 1280x720 -ar 44100 -async 44100 -r 29.970 -ac 2 -qscale 5 '.$converted_file;
                    echo exec($ffmpeg_command);
                    $sql = "UPDATE pm_temp SET url = '".$conv_name."' WHERE url = '".$new_name."' LIMIT 1";
                    $result = @mysql_query($sql);
                    unlink($convert_source);    
                }

This code to convert avi to mp4 ffmpeg concole output:

root@1tb:~# ffmpeg -i sample.avi -acodec libmp3lame -vcodec libx264 -s 1280x720 -ar 44100 -async 44100 -r 29.970 -ac 2 -qscale 5 goodsample.mp4
ffmpeg version 0.7.15, Copyright (c) 2000-2013 the FFmpeg developers
  built on Feb 22 2013 07:18:58 with gcc 4.4.5
  configuration: --enable-libdc1394 --prefix=/usr --extra-cflags='-Wall -g ' --cc='ccache cc' --enable-shared --enable-libmp3lame --enable-gpl --enable-libvorbis --enable-pthreads --enable-libfaac --enable-libxvid --enable-postproc --enable-x11grab --enable-libgsm --enable-libtheora --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libx264 --enable-libspeex --enable-nonfree --disable-stripping --enable-avfilter --enable-libdirac --disable-decoder=libdirac --enable-libfreetype --enable-libschroedinger --disable-encoder=libschroedinger -                                                                                                                                                             s
  libavutil    50. 43. 0 / 50. 43. 0
  libavcodec   52.123. 0 / 52.123. 0
  libavformat  52.111. 0 / 52.111. 0
  libavdevice  52.  5. 0 / 52.  5. 0
  libavfilter   1. 80. 0 /  1. 80. 0
  libswscale    0. 14. 1 /  0. 14. 1
  libpostproc  51.  2. 0 / 51.  2. 0
[mp3 @ 0x191d4100] Header missing
[mpeg4 @ 0x191d1dc0] Invalid and inefficient vfw-avi packed B frames detected
Input #0, avi, from 'sample.avi':
  Metadata:
    encoder         : VirtualDubMod 1.5.10.2 (build 2540/release)
  Duration: 00:01:01.81, start: 0.000000, bitrate: 1194 kb/s
    Stream #0.0: Video: mpeg4, yuv420p, 640x352 [PAR 1:1 DAR 20:11], 23.98 tbr,
    Stream #0.1: Audio: mp3, 48000 Hz, stereo, s16, 128 kb/s
[buffer @ 0x191d1c80] w:640 h:352 pixfmt:yuv420p tb:1/1000000 sar:1/1 sws_param:
[scale @ 0x191d6880] w:640 h:352 fmt:yuv420p -> w:1280 h:720 fmt:yuv420p flags:0
[libx264 @ 0x191ce5a0] Default settings detected, using medium profile
[libx264 @ 0x191ce5a0] using SAR=45/44
[libx264 @ 0x191ce5a0] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle S
[libx264 @ 0x191ce5a0] profile High, level 3.1
[libx264 @ 0x191ce5a0] 264 - core 118 - H.264/MPEG-4 AVC codec - Copyleft 2003-2                                                                                                                                                             6 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_off                                                                                                                                                             1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_l
Output #0, mp4, to 'goodsample.mp4':
  Metadata:
    encoder         : Lavf52.111.0
    Stream #0.0: Video: libx264, yuv420p, 1280x720 [PAR 45:44 DAR 20:11], q=2-31
    Stream #0.1: Audio: libmp3lame, 44100 Hz, stereo, s16, 64 kb/s
Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1
Press [q] to stop, [?] for help
[mp3 @ 0x191d4100] Header missing
Error while decoding stream #0.1
[mpeg4 @ 0x191d1dc0] Invalid and inefficient vfw-avi packed B frames detected
[mp3 @ 0x191d4100] incomplete frame 9467kB time=00:01:00.32 bitrate=1285.5kbits/
Error while decoding stream #0.1
frame= 1852 fps= 20 q=29.0 Lsize=    9652kB time=00:01:01.72 bitrate=1280.9kbits
video:9121kB audio:483kB global headers:0kB muxing overhead 0.499688%
frame I:11    Avg QP:16.78  size: 51456
[libx264 @ 0x191ce5a0] frame P:784   Avg QP:20.81  size:  8954
[libx264 @ 0x191ce5a0] frame B:1057  Avg QP:26.06  size:  1659
[libx264 @ 0x191ce5a0] consecutive B-frames: 22.0%  3.1%  7.5% 67.4%
[libx264 @ 0x191ce5a0] mb I  I16..4: 31.1% 59.8%  9.1%
[libx264 @ 0x191ce5a0] mb P  I16..4:  1.8%  2.6%  0.2%  P16..4: 24.3%  7.0%  4.0
[libx264 @ 0x191ce5a0] mb B  I16..4:  0.1%  0.1%  0.0%  B16..8: 22.7%  0.8%  0.2
[libx264 @ 0x191ce5a0] 8x8 transform intra:57.0% inter:72.6%
[libx264 @ 0x191ce5a0] coded y,uvDC,uvAC intra: 44.4% 33.3% 10.3% inter: 7.6% 5.
[libx264 @ 0x191ce5a0] i16 v,h,dc,p: 68% 14%  8% 10%
[libx264 @ 0x191ce5a0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 21% 14% 27%  5%  7%  7%  6
[libx264 @ 0x191ce5a0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 28% 14% 14%  6% 10%  9%  7
[libx264 @ 0x191ce5a0] i8c dc,h,v,p: 67% 13% 17%  3%
[libx264 @ 0x191ce5a0] Weighted P-Frames: Y:1.9% UV:0.4%
[libx264 @ 0x191ce5a0] ref P L0: 62.2% 12.8% 10.3% 14.5%  0.2%
[libx264 @ 0x191ce5a0] ref B L0: 88.1%  5.5%  6.4%
[libx264 @ 0x191ce5a0] ref B L1: 95.7%  4.3%
[libx264 @ 0x191ce5a0] kb/s:1209.03

I know there is couple errors tough, but i dont know hot to fix it. Also i would be very thankfull if someone can help reduce video size but is not main problem video weights as original avi but sill.