Тестовые стенды: 
p10 workstation / education / kworkstation x86_64

libflatpak-1.10.2-alt2.x86_64
flatpak-1.10.2-alt2.x86_64

1) Добавить репозиторий:
$ flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
2) Выполнить установку приложения из репозитория:
$ flatpak install flathub com.uploadedlobster.peek
3) Проверить запуск:
$ flatpak run com.uploadedlobster.peek
Нажать "Записать как GIF", дождаться 3-2-1.

Результат: появляется ошибка записи.

Command "ffmpeg -f x11grab -show_region 0 -framerate 10 -video_size 498x298 -i :99.0+150,180 -filter:v scale=iw/1:-1 -codec:v libvpx-vp9 -lossless 1 -r 10 -y /home/test/.var/app/com.uploadedlobster.peek/cache/peek/peekUGWR90.webm" failed with status 256 (received signal 0).
Output:
ffmpeg version 4.3.1 Copyright (c) 2000-2020 the FFmpeg developers  built with gcc 10.2.0 (GCC)  configuration: --prefix=/app --disable-debug --disable-static --enable-gpl --enable-libvpx --enable-libx264 --enable-shared --enable-libxcb --enable-libxcb-xfixes --disable-libxcb-shape --disable-ffplay --disable-ffprobe --disable-doc --disable-everything --enable-bsf=vp9_superframe --enable-decoder=libvpx_vp9 --enable-decoder=png --enable-decoder=rawvideo --enable-encoder=apng --enable-encoder=ffvhuff --enable-encoder=gif --enable-encoder=libvpx_vp9 --enable-encoder=libx264 --enable-encoder=png --enable-demuxer=image2 --enable-demuxer=matroska --enable-muxer=apng --enable-muxer=gif --enable-muxer=image2 --enable-muxer=mp4 --enable-muxer=webm --enable-filter=crop --enable-filter=fps --enable-filter=palettegen --enable-filter=paletteuse --enable-filter=scale --enable-protocol=file --enable-indev=xcbgrab  libavutil      56. 51.100 / 56. 51.100  libavcodec     58. 91.100 / 58. 91.100  libavformat    58. 45.100 / 58. 45.100  libavdevice    58. 10.100 / 58. 10.100  libavfilter     7. 85.100 /  7. 85.100  libswscale      5.  7.100 /  5.  7.100  libswresample   3.  7.100 /  3.  7.100  libpostproc    55.  7.100 / 55.  7.100Input #0, x11grab, from ':99.0+150,180':  Duration: N/A, start: 1631691252.344432, bitrate: 47489 kb/s    Stream #0:0: Video: rawvideo (BGR[0] / 0x524742), bgr0, 498x298, 47489 kb/s, 10 fps, 10 tbr, 1000k tbn, 1000k tbcStream mapping:  Stream #0:0 -> #0:0 (rawvideo (native) -> vp9 (libvpx-vp9))Press [q] to stop, [?] for help[libvpx-vp9 @ 0x557356122000] v1.10.0[libvpx-vp9 @ 0x557356122000] Failed to initialize encoder: ABI version mismatchError initializing output stream 0:0 -- Error while opening encoder for output stream #0:0 - maybe incorrect parameters such as bit_rate, rate, width or heightConversion failed!

Ожидаемый результат: успешная запись