I can confirm this bug exists on Debian Wheezy amd64, but does NOT exist on Debian Wheezy kfreebsd_amd64.
On the Debian Wheezy amd64 (linux) machine:
plus@honoka:~$ wavpack -b400 -c -m hybrid.wav
WAVPACK Hybrid Lossless Audio Compressor Linux Version 4.60.1
Copyright (c) 1998 - 2009 Conifer Software. All Rights Reserved.
original md5 signature: e180f2ec2c4c65fd214bc6c4f70c7988
created hybrid.wv (+.wvc) in 0.38 secs (lossless, 41.39%)
plus@honoka:~$ wvunpack -m hybrid.wv
WVUNPACK Hybrid Lossless Audio Decompressor Linux Version 4.60.1
Copyright (c) 1998 - 2009 Conifer Software. All Rights Reserved.
overwrite hybrid.wav (yes/no/all)? yes
original md5: e180f2ec2c4c65fd214bc6c4f70c7988
unpacked md5: 2d5edeb0d3d7ba971282428b77fd41c6
MD5 signatures should match, but do not!
On the Debian Wheezy kfreebsd_amd64 machine:
eric@nene:~$ wavpack -b400 -c -m hybrid.wav
WAVPACK Hybrid Lossless Audio Compressor GNU/kFreeBSD Version 4.60.1
Copyright (c) 1998 - 2009 Conifer Software. All Rights Reserved.
original md5 signature: e180f2ec2c4c65fd214bc6c4f70c7988
created hybrid.wv (+.wvc) in 0.47 secs (lossless, 39.23%)
eric@nene:~$ wvunpack -m hybrid.wv
WVUNPACK Hybrid Lossless Audio Decompressor GNU/kFreeBSD Version 4.60.1
Copyright (c) 1998 - 2009 Conifer Software. All Rights Reserved.
overwrite hybrid.wav (yes/no/all)? yes
original md5: e180f2ec2c4c65fd214bc6c4f70c7988
unpacked md5: e180f2ec2c4c65fd214bc6c4f70c7988
restored hybrid.wav in 0.35 secs (lossless, 39.23%)
Both computers are running the latest version of wavpack in the Debian repositories.