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I think your problem is not a opencv problem but I hope this answer will help you.

In this program I make a screen copy at 20 fps and send image to ffmpeg. i don't use pipe but socket. I use this command line :

ffmpeg -f rawvideo -pixel_format rgb24  -video_size 640x480 -i  "tcp://127.0.0.1:2345" -codec:v libx264 -pix_fmt yuv420p Video.mp4

to run ffmpeg and then send data to port 2345 using socket

    sock->Write(b.GetData(), nb);

I don't encode frame it is raw data