@gorman This may or may not be relevant. But your ffmpeg version is ancient (by ffmpeg standards).
I don't know how fb2k behaves. But everything seems to be working as expected here:
% ffmpeg -i t.flac t.opus
ffmpeg version N-86873-g9f449227a3 Copyright (c) 2000-2017 the FFmpeg developers
built with gcc 7.1.1 (GCC) 20170630
configuration: --prefix=/usr --enable-gpl --enable-nonfree --enable-version3 --enable-avresample --enable-openssl --enable-libmp3lame --enable-libspeex --enable-libx264 --enable-libx265 --enable-libxvid --enable-libvpx --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libtheora --enable-libvorbis --enable-libfdk-aac --enable-libopus --enable-libsoxr --enable-libass --enable-libopenjpeg --enable-libfreetype --enable-libfribidi --enable-libvidstab --enable-libwavpack --enable-libbluray --enable-frei0r --enable-shared --enable-pthreads --enable-pic --disable-static --disable-debug --enable-runtime-cpudetect
libavutil 55. 69.100 / 55. 69.100
libavcodec 57.102.100 / 57.102.100
libavformat 57. 76.100 / 57. 76.100
libavdevice 57. 7.100 / 57. 7.100
libavfilter 6. 95.100 / 6. 95.100
libavresample 3. 6. 0 / 3. 6. 0
libswscale 4. 7.101 / 4. 7.101
libswresample 2. 8.100 / 2. 8.100
libpostproc 54. 6.100 / 54. 6.100
Input #0, flac, from 't.flac':
Metadata:
ENCODER : Lavf57.76.100
REPLAYGAIN_ALBUM_GAIN: -12.54 dB
REPLAYGAIN_ALBUM_PEAK: 1.000000
REPLAYGAIN_TRACK_GAIN: -12.54 dB
REPLAYGAIN_TRACK_PEAK: 1.000000
Duration: 00:05:53.14, start: 0.000000, bitrate: 1764 kb/s
Stream #0:0: Audio: flac, 48000 Hz, stereo, s32 (24 bit)
Side data:
replaygain: track gain - -12.540000, track peak - 0.000023, album gain - -12.540000, album peak - 0.000023,
Stream mapping:
Stream #0:0 -> #0:0 (flac (native) -> opus (libopus))
Press [q] to stop, [?] for help
[libopus @ 0x558fecb5af00] No bit rate set. Defaulting to 96000 bps.
Output #0, opus, to 't.opus':
Metadata:
REPLAYGAIN_TRACK_PEAK: 1.000000
REPLAYGAIN_ALBUM_GAIN: -12.54 dB
REPLAYGAIN_ALBUM_PEAK: 1.000000
REPLAYGAIN_TRACK_GAIN: -12.54 dB
encoder : Lavf57.76.100
Stream #0:0: Audio: opus (libopus), 48000 Hz, stereo, flt (24 bit), 96 kb/s
Metadata:
encoder : Lavc57.102.100 libopus
REPLAYGAIN_TRACK_PEAK: 1.000000
REPLAYGAIN_ALBUM_GAIN: -12.54 dB
REPLAYGAIN_ALBUM_PEAK: 1.000000
REPLAYGAIN_TRACK_GAIN: -12.54 dB
Side data:
replaygain: track gain - -12.540000, track peak - 0.000023, album gain - -12.540000, album peak - 0.000023,
size= 4125kB time=00:05:53.15 bitrate= 95.7kbits/s speed=47.2x
video:0kB audio:4094kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.749829%
% opusinfo t.opus
Processing file "t.opus"...
New logical stream (#1, serial: 56aa41e5): type opus
Encoded with Lavf57.76.100
User comments section follows...
encoder=Lavc57.102.100 libopus
REPLAYGAIN_TRACK_PEAK=1.000000
REPLAYGAIN_ALBUM_GAIN=-12.54 dB
REPLAYGAIN_ALBUM_PEAK=1.000000
REPLAYGAIN_TRACK_GAIN=-12.54 dB
Opus stream 1:
Pre-skip: 312
Playback gain: 0 dB
Channels: 2
Original sample rate: 48000Hz
Packet duration: 20.0ms (max), 20.0ms (avg), 20.0ms (min)
Page duration: 1000.0ms (max), 997.6ms (avg), 160.0ms (min)
Total data length: 4224125 bytes (overhead: 0.744%)
Playback length: 5m:53.135s
Average bitrate: 95.69 kb/s, w/o overhead: 94.98 kb/s
Logical stream 1 ended