CPU: Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
Memory: 8 GB
OS: Lubuntu 12.10
Package: libsndfile-1.0.25-5 (from distribution)
The problem is described in the subject line.
Here's output from sndfile-info for one FLAC file that this occurs with:
Version : libsndfile-1.0.25
File : instrument1-layer1.flac
Length : 86188
FLAC Stream Metadata
Channels : 2
Sample rate : 48000
Frames : 20097
Bit width : 24
Vorbis Comment Metadata
End
Sample Rate : 48000
Frames : 20097
Channels : 2
Format : 0x00170003
Sections : 1
Seekable : TRUE
Duration : 00:00:00.419
Signal Max : 2.79467e+06 (-9.55 dB)
Note that the FLAC file referenced above was written using libsndfile.
I suspect the problem might be here:
https://github.com/erikd/libsndfile/blob/master/src/flac.c#L1346
... but I've done nothing to confirm it yet.