I am currently using Kdenlive, but have also used ffmpeg when I have the simple task of adding audio to a video that does not yet have audio. Since it is just a matter of putting the video file together with the audio, it seems like it ought to be simple. Is there something about encoding mp4's that means it must take a lot of processing to complete?
I have good hardware (i7 6700k and gtx 1080), but kdenlive currently estimates 2.5 hours to complete adding audio to a 10 minute video.