I just had a look at this in jessie with cuetools 1.4.0-2

I copied the sample TOC into a file called test1.toc and executed:

$ cueconvert test1.toc > test1.cue

and observe the same fault in test1.cue

Then I tried adapting the TOC with the sed script[1]

$ cat test1.toc | sed -f tocfix.sed > test1-with-START.toc

$ cueconvert test1-with-START.toc > test2.cue

and test2.cue appears different (is it correct?):

CATALOG 0042284361422

FILE "cousteau-2006-11-19.21:11:15-13112.bin" WAVE
TRACK 01 AUDIO
INDEX 00 00:00:00
INDEX 01 00:00:33
INDEX 02 04:11:07
INDEX 03 05:09:37

TRACK 02 AUDIO
INDEX 01 08:23:50
INDEX 02 12:29:05

TRACK 03 AUDIO
INDEX 01 15:34:25

TRACK 04 AUDIO
INDEX 00 22:03:60
INDEX 01 22:05:05


I feel the script name tocfix.sed is slightly misleading, the TOC is not
actually broken, maybe toc-workaround.sed may be more precise.

Upstream cueconvert is now on Github[2] so maybe it is possible for
somebody to make a pull request to finally fix it

1.
https://anonscm.debian.org/cgit/pkg-multimedia/flactag.git/tree/tocfix.sed

2. https://github.com/svend/cuetools

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