Problem solved , strange but i tell you what the problem was and how to solve it.
If you have Centos5 and apache, and if you install ffmpeg with ( yum install "something" ) option then you should experience a badly installed mencoder , as it can't convert through php, only in shell.
All you have to do is install the latest mplayer.

There is another problem, that's why i couldn't solve it first. The best is to install ffmpeg one by one and not using yum, but on 8th September 2008 a new API ffmpeg came out, and ffmpeg-php is not supporting it. I couldn't get an older ffmpeg, that's why i used yum install, but then it lead to the problem mentioned above.But all solved now with installing the latest mplayer.But be sure NOT to install latest ffmpeg, as it does not go with latest ffmpeg-php which is: ffmpeg-php-0.5.3.1 . So those who want to install latest api, have to wait for a newer ffmpeg-php to come out , or install older ffmpeg.Hope it helps others!