Why does this:

$ ffmpeg -y -lowres 1 -r 24 -r 24 -i left/001_%06dL.j2c [...]

yield

Input #0, image2, from 'left/001_%06dL.j2c':
[...] 25 fps, 25 tbr, 25 tbn, 25 tbc

?

$ ffmpeg -y -lowres 1 -r 24 -r 24 -i left/001_%06dL.j2c -r 24 -i audio/mayday_nowhere.wav -crf 18 -c:a ac3 -r 24 -pix_fmt yuv420p -vf "crop=1024:428:0:0" mayday_nowhere-left_eye-r1.mov
ffmpeg version N-56198-gbbcaf25 Copyright (c) 2000-2013 the FFmpeg developers
  built on Sep 12 2013 13:08:54 with gcc 4.6 (Ubuntu/Linaro 4.6.3-1ubuntu5)
  configuration: --extra-ldflags=-L/home/yusari/.digital_cinema_tools/.lib/openjpeg/openjpeg-1.5.0/libopenjpeg/.libs --extra-cflags=-I/home/yusari/.digital_cinema_tools/.lib/openjpeg/openjpeg-1.5.0/libopenjpeg --enable-libopenjpeg --enable-libfreetype --enable-gpl --enable-libx264 --prefix=/home/yusari/local
  libavutil      52. 43.100 / 52. 43.100
  libavcodec     55. 31.101 / 55. 31.101
  libavformat    55. 16.102 / 55. 16.102
  libavdevice    55.  3.100 / 55.  3.100
  libavfilter     3. 84.100 /  3. 84.100
  libswscale      2.  5.100 /  2.  5.100
  libswresample   0. 17.103 /  0. 17.103
  libpostproc    52.  3.100 / 52.  3.100
Input #0, image2, from 'left/001_%06dL.j2c':
  Duration: 01:57:03.84, start: 0.000000, bitrate: N/A
    Stream #0:0: Video: jpeg2000 (JPEG 2000 digital cinema 2K), xyz12le, 1024x429, 25 fps, 25 tbr, 25 tbn, 25 tbc
Guessed Channel Layout for  Input Stream #1.0 : 5.1
Input #1, wav, from 'audio/mayday_nowhere.wav':
  Duration: 02:01:56.50, bitrate: 6912 kb/s
    Stream #1:0: Audio: pcm_s24le ([1][0][0][0] / 0x0001), 48000 Hz, 5.1, s32, 6912 kb/s
[swscaler @ 0x1bac040] deprecated pixel format used, make sure you did set range correctly
[libx264 @ 0x1c7cae0] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
[libx264 @ 0x1c7cae0] profile High, level 3.1
[libx264 @ 0x1c7cae0] 264 - core 135 r2 f0c1c53 - H.264/MPEG-4 AVC codec - Copyleft 2003-2013 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=24 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=18.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mov, to 'mayday_nowhere-left_eye-r1.mov':
  Metadata:
    encoder         : Lavf55.16.102
    Stream #0:0: Video: h264 (libx264) (avc1 / 0x31637661), yuv420p, 1024x428, q=-1--1, 12288 tbn, 24 tbc
    Stream #0:1: Audio: ac3 (ac-3 / 0x332D6361), 48000 Hz, 5.1, fltp, 448 kb/s
Stream mapping:
  Stream #0:0 -> #0:0 (jpeg2000 -> libx264)
  Stream #1:0 -> #0:1 (pcm_s24le -> ac3)