Video upload ffmpeg problem

I know this appears to be a long standing topic, but I need to get around this problem of videos not uploading.
I have set all the correct file permissions, have the php settings correct and after upload I just get a video file sat in pending when I go to dolphin admin/videos.

I have waited for the video to process, e.g 25mb flv file, a day later nothing!
I have another site that is much like a youtube clone and video uploads work perfectly none of this waiting for hours or all the messing around.

Oh, I am also on VPS hosting which also host my other youtube clone site that works fine with ffmpeg, so its certainly not my hosts limitations.

Has anyone figured out a fix for this as yet, I am keen to get some feedback from others who may have run into this and have managed to fix it.

Thanks : )

Have you configured your cron job?