The media-video/handbrake ebuild requires media-libs/zimg, but if ffmpeg is not built with the zimg USE flag, the zscale filter is not able to be loaded (since ffmpeg won't know about zimg and hence the zscale filter). The relevant error appears in log files in ~/.config/ghb/EncodeLogs/, the error if ffmpeg is not built with the zimg is [AVFilterGraph @ 0x7f33d0056cc0] No such filter: 'zscale' [AVFilterGraph @ 0x7f33d0056cc0] Error creating filters [14:06:06] hb_avfilter_graph_init: avfilter_graph_parse2 failed (crop='x=0:y=74:w=720:h=428',zscale='width=720:height=428:filter=lanczos',format='pix_fmts=yuv420p') [14:06:06] Failure to initialise filter 'AVFilter', disabling Times and memory addresses may differ, but the result (in my case) is that the video isn't cropped, but is shifted (as if the cropping was done) which is how I noticed the issue initially. Simply recompiling ffmpeg with the zimg USE flag enabled is enough to fix this issue.