I am using the ffmpeg that is installed as part of Ubuntu 16.04 - no
special build.
Log of conversion using ffmpeg so that version and decoders are shown 

Code:
--------------------
    
  xxx@minitower:/tmp$ ffmpeg -loglevel info -i /home/xxxx/Downloads/lastr.mod 
-f flac lastr.flc
  ffmpeg version 3.3.3-2~ubuntu16.04.1~ppa1 Copyright (c) 2000-2017 the FFmpeg 
developers
  built with gcc 5.4.0 (Ubuntu 5.4.0-6ubuntu1~16.04.4) 20160609
  configuration: --prefix=/usr --extra-version='2~ubuntu16.04.1~ppa1' 
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu 
--incdir=/usr/include/x86_64-linux-gnu --enable-gpl --disable-stripping 
--enable-avresample --enable-avisynth --enable-gnutls --enable-ladspa 
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca 
--enable-libcdio --enable-libflite --enable-libfontconfig --enable-libfreetype 
--enable-libfribidi --enable-libgme --enable-libgsm --enable-libmp3lame 
--enable-libopenjpeg --enable-libopenmpt --enable-libopus --enable-libpulse 
--enable-librubberband --enable-libshine --enable-libsnappy --enable-libsoxr 
--enable-libspeex --enable-libssh --enable-libtheora --enable-libtwolame 
--enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp 
--enable-libx265 --enable-libxvid --enable-libzmq --enable-libzvbi --enable-omx 
--enable-openal --enable-opengl --enable-sdl2 --enable-libdc1394 
--enable-libiec61883 --enable-chromaprint --enable-frei0r -
 -enable-libopencv --enable-libx264 --enable-shared
  libavutil      55. 58.100 / 55. 58.100
  libavcodec     57. 89.100 / 57. 89.100
  libavformat    57. 71.100 / 57. 71.100
  libavdevice    57.  6.100 / 57.  6.100
  libavfilter     6. 82.100 /  6. 82.100
  libavresample   3.  5.  0 /  3.  5.  0
  libswscale      4.  6.100 /  4.  6.100
  libswresample   2.  7.100 /  2.  7.100
  libpostproc    54.  5.100 / 54.  5.100
  Guessed Channel Layout for Input Stream #0.0 : stereo
  Input #0, libopenmpt, from '/home/xxxx/Downloads/lastr.mod':
  Metadata:
  title           : last roundabout
  encoder         : ProTracker / NoiseTracker / Soundtracker / SoundTracker 2.6 
/ Ice Tracker / Mod's Grave
  comment         : (c) 1992 jesper kyd
  : finished the 25-10-92
  : composed for the...
  : sound of silents ii
  : skinny3
  : skinny4=5(3)
  : skinny2
  : freak23
  : freak17
  : freak12
  : 
  : synth
  : 
  : 
  : 
  : overbazz
  : overbazz2
  : cguit
  : eu2
  : 
  : strings2
  : 
  : strings1
  : 
  : 
  : 
  : 
  : 
  : 
  : 
  : 
  : 
  Duration: 00:08:02.66, bitrate: 3 kb/s
  Stream #0:0: Audio: pcm_f32le, 48000 Hz, stereo, flt, 3072 kb/s
  Stream mapping:
  Stream #0:0 -> #0:0 (pcm_f32le (native) -> flac (native))
  Press [q] to stop, [?] for help
  [flac @ 0x556c80372580] encoding as 24 bits-per-sample
  Output #0, flac, to 'lastr.flc':
  Metadata:
  title           : last roundabout
  DESCRIPTION     : (c) 1992 jesper kyd
  : finished the 25-10-92
  : composed for the...
  : sound of silents ii
  : skinny3
  : skinny4=5(3)
  : skinny2
  : freak23
  : freak17
  : freak12
  : 
  : synth
  : 
  : 
  : 
  : overbazz
  : overbazz2
  : cguit
  : eu2
  : 
  : strings2
  : 
  : strings1
  : 
  : 
  : 
  : 
  : 
  : 
  : 
  : 
  : 
  encoder         : Lavf57.71.100
  Stream #0:0: Audio: flac, 48000 Hz, stereo, s32 (24 bit), 128 kb/s
  Metadata:
  encoder         : Lavc57.89.100 flac
  size=   87181kB time=00:08:02.77 bitrate=1479.3kbits/s speed= 157x    
  video:0kB audio:87172kB subtitle:0kB other streams:0kB global headers:0kB 
muxing overhead: 0.009557%
  
--------------------


For completeness the conf file that could work would be like the
following. There will be issues like LMS will not able to scan the file
so duration etc will not be known so conversion to flac would be an
overall better solution.
custom-types.conf

Code:
--------------------
    
  mod mp3 * *
        # F:{PATH=%f}R:{PATH=%F}B:{BITRATE=-B %B}T:{START=-ss %s}
        [ffmpeg] -loglevel quiet  -i $PATH$ -f wav - | [lame] --silent -q 
$QUALITY$ $BITRATE$ - -
  
  mod pcm * *
        # F:{PATH=%f}R:{PATH=%F}B:{BITRATE=-B %B}T:{START=-ss %s}
        [ffmpeg] -loglevel quiet  -i $PATH$ -f u16le -
  
  mod flc * *
        # F:{PATH=%f}R:{PATH=%F}B:{BITRATE=-B %B}T:{START=-ss %s}
        [ffmpeg] -loglevel quiet -i $PATH$ -f flac -
  
  
--------------------

custom-convert.conf

Code:
--------------------
    
  mod    mod           -                               audio
  
--------------------

custom-strings.txt

Code:
--------------------
    
  MOD
        EN      Amiga MOD audio
  
--------------------


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