How do I prevent Quality loss in the beginning of a video? My company transcodes videos sent in by users (recorder by our own screenrecording software)

I use FFMpeg to do the work using this command:

 /ffmpeg/ffmpeg -i in.mov -vcodec libx264 -fpre /ffmpeg/ffpresets/libx264-slower.ffpreset   -y out.flv


The purpose is to prepare the video for viewing in browser.

The problem is that the first 10, or so, seconds the quality is really poor.

What can cause this? and how can i fix it?

Preset settings:

coder=1
flags=+loop
cmp=+chroma
partitions=+parti8x8+parti4x4+partp8x8+partb8x8
me_method=umh
subq=8
me_range=16
g=250
keyint_min=25
sc_threshold=40
i_qfactor=0.71
b_strategy=2
qcomp=0.6
qmin=0
qmax=69
qdiff=4
bf=3
refs=5
directpred=3
trellis=1
flags2=+bpyramid+mixed_refs+wpred+dct8x8+fastpskip
wpredp=2
rc_lookahead=50


Exampel of an input video

Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '84f42bcb67ac616635ef6f99057bbbc46d418295.mov':
Metadata:
    major_brand     : qt
    minor_version   : 537199360
    compatible_brands: qt
    creation_time   : 2012-03-07 13:45:16
  Duration: 00:15:56.00, start: 0.000000, bitrate: 4108 kb/s
    Stream #0.0(eng): Video: qtrle, rgb24, 1680x945, 3401 kb/s, 13.61 fps, 1k tbr, 1k tbn, 1k tbc
    Metadata:
      creation_time   : 2012-03-07 13:45:16
    Stream #0.1(eng): Audio: pcm_s16be, 44100 Hz, 1 channels, s16, 705 kb/s
    Metadata:
      creation_time   : 2012-03-07 13:45:16
Fixed by updating FFMpeg to newer version