Encoding a certain set of WAV files produces FLACs that verify correctly, but that are noisy/distorted, or fail to play, when I play them in certain players. Different compression levels make no difference.
Why do I think this is a FLAC bug and not a bug with the player(s) in question? Well, the WAVs themselves plays fine, and if I decode the FLAC to a new file, that too plays fine. But playing the FLAC itself? Results vary, as follows:
* I get the distorted sound from several players (Amarok, Bangarang, Dolphin's preview player), though I think they all use the same KDE playback backend.
* VLC actually gives me no sound whatsoever.
* Mplayer plays without distortion. But...
The other noteworthy thing is that in every player, whatever I hear, it doesn't last as long as the original file. I've created a snippet  of one of the files and encoded it; the WAV is about 11 seconds, but the FLAC  goes silent after less than a second and stops playing after about 6 seconds.
Also, a FLAC encoded with flake 0.11  works fine, but the encoder complains about the result not being lossless:
Flake: FLAC audio encoder
(c) 2006-2007 Justin Ruggles
WARNING! The chosen encoding options are
not FLAC Subset compliant. Therefore, the
encoded file(s) may not work properly with
some FLAC players and decoders.
block time: 105ms
variable block size: none
prediction type: levinson-durbin
prediction order: 1,8
partition order: 0,6
order method: estimate
stereo method: mid-side
header padding: 4096
input file: "battle1.wav"
output file: "battle1.flac"
Unsigned 8-bit 11025 Hz stereo
WARNING! converting to 16-bit (not lossless)
samples: 1559548 (2m21.455s)
block size: 1152
Version and system info:
* flac 1.2.1
* Kubuntu 10.10 (Linux 2.6.35-23-generic, KDE SC 4.5.1)
* Intel Core2 Duo E7400
The WAV files are fairly old (from the soundtrack of 1996 game "Lords of the Realm II"), so maybe there's something unusual about their format; wavinfo  gives me this information for one of the files:
Header info for: battle1.wav
WaveHeader Size: 12
ChunkHeader Size: 8
FormatChunk Size: 16
RIFF ID: RIFF
Total Size: 3119132
Wave ID: WAVE
Chunk ID: fmt
Chunk Size: 16
Compression format is of type: 1
Sample Rate: 11025
Bytes / Sec: 22050
Bits Per Sample Point: 8
 Even snipped, it's just slightly too large to upload, but decoding the attachment should recover it correctly
 See attachment