CRON Error - MySQL server has gone away

Seems stream 1 codec frame rate differs from container frame rate: 1000.00 (1000/1) -> 29.97 (30000/1001)
Input #0, asf, from '/home/fdd/public_html/fdd/flash/modules/video/files/4':
  Metadata:
    Application     : Windows Movie Maker 2.6.4037.0
    WM/ParentalRating: 
    WMFSDKVersion   : 12.0.7601.17514
    WMFSDKNeeded    : 0.0.0.0000
    IsVBR           : 0
    title           : 
    author          : 
    copyright       : 
    comment         : 
  Duration: 00:01:03.25, start: 1.579000, bitrate: 1570 kb/s
    Stream #0.0: Audio: wmav2, 44100 Hz, 2 channels, s16, 160 kb/s
    Stream #0.1: Video: wmv3, yuv420p, 720x480, 29.97 tbr, 1k tbn, 1k tbc
[wmv3 @ 0x9c9f4e0]Extra data: 8 bits left, value: 0
Output #0, mp4, to '/home/fdd/public_html/fdd/flash/modules/video/files/4.mp4':
  Metadata:
    encoder         : Lavf52.64.2
    Stream #0.0: Video: mpeg4, yuv420p, 176x144, q=2-31, 512 kb/s, 25 tbn, 25 tbc
    Stream #0.1: Audio: libfaac, 44100 Hz, 1 channels, s16, 128 kb/s
Stream mapping:
  Stream #0.1 -> #0.0
  Stream #0.0 -> #0.1
Press [q] to stop encoding
frame=  114 fps=  0 q=0.0 size=     122kB time=4.56 bitrate= 218.5kbits/s dup=0 drop=22    
frame=  235 fps=232 q=0.0 size=     266kB time=9.40 bitrate= 231.4kbits/s dup=0 drop=46    
frame=  359 fps=237 q=0.0 size=     402kB time=14.36 bitrate= 229.3kbits/s dup=0 drop=71    
frame=  489 fps=243 q=0.0 size=     512kB time=19.56 bitrate= 214.4kbits/s dup=0 drop=97    
frame=  617 fps=245 q=0.0 size=     651kB time=24.68 bitrate= 216.1kbits/s dup=0 drop=122    
frame=  759 fps=252 q=0.0 size=     745kB time=30.36 bitrate= 201.0kbits/s dup=0 drop=151    
frame=  877 fps=249 q=0.0 size=     859kB time=35.08 bitrate= 200.5kbits/s dup=0 drop=174    
frame=  988 fps=246 q=0.0 size=     976kB time=39.52 bitrate= 202.4kbits/s dup=0 drop=196    
frame= 1134 fps=251 q=0.0 size=    1079kB time=45.36 bitrate= 194.8kbits/s dup=0 drop=225    
frame= 1253 fps=249 q=0.0 size=    1210kB time=50.12 bitrate= 197.8kbits/s dup=0 drop=249    
frame= 1382 fps=250 q=0.0 size=    1433kB time=55.28 bitrate= 212.3kbits/s dup=0 drop=274    
frame= 1495 fps=248 q=0.0 size=    1825kB time=59.80 bitrate= 250.0kbits/s dup=0 drop=297    
frame= 1581 fps=246 q=0.0 Lsize=    2150kB time=63.23 bitrate= 278.6kbits/s dup=0 drop=314    
video:2099kB audio:16kB global headers:0kB muxing overhead 1.668897% Database access error. Description: MySQL server has gone away

What are your php.ini time out settings?

In the flash admin>video there is a setting for .h264 encoding, that should be turned off as well.