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Let me reproduce the bugreport I sent to the Debian bug-tracking system:

Subject: oggenc: --output=FILE and >FILE have different results
Package: vorbis-tools
Version: 1.0rc3-1
Severity: important

oggenc seems to create different files depending on the style of the
commandline, whether it is

$ cat test.raw | oggenc --raw - --output=test-inputpipe.ogg

or

$ cat test.raw | oggenc --raw - > test-pipe.ogg

The big trouble is that the latter method (> FILE) produces a file
that ogg123 can read without any visible error/warning, but ogginfo
says that the integrity test fails, and vorbiscomment doesn't even
recognize the file as a Ogg file.

An example should make this clearer:

================================================================
*** First, we create the files.

$ oggenc --raw test.raw --output=test.ogg
Encoding "test.raw" to 
         "test.ogg" at quality 3,00
Encoding with VBR
	Encoding [ 1m39s so far] -

Done encoding file "test.ogg"

	File length:  1m 01,0s
	Elapsed time: 1m 40,2s
	Rate:         0,6183
	Average bitrate: 84,1 kb/s

$ cat test.raw | oggenc --raw - > test-pipe.ogg
Encoding standard input to 
         standard output at quality 3,00
	Encoding [ 1m48s so far] -

Done encoding.

	File length:  1m 01,0s
	Elapsed time: 1m 49,1s
	Rate:         0,5675
	Average bitrate: 84,1 kb/s

$ cat test.raw | oggenc --raw - --output=test-inputpipe.ogg
Encoding standard input to 
         "test-inputpipe.ogg" at quality 3,00
Encoding with VBR
	Encoding [ 1m40s so far] -

Done encoding file "test-inputpipe.ogg"

	File length:  1m 01,0s
	Elapsed time: 1m 41,0s
	Rate:         0,6132
	Average bitrate: 84,1 kb/s

*** Now, we try these files:

$ ogginfo test.ogg
filename=test.ogg

serial=1963857601
header_integrity=pass
vendor=Xiphophorus libVorbis I 20011231
version=0
channels=2
rate=44100
bitrate_upper=none
bitrate_nominal=112015
bitrate_lower=none
stream_integrity=pass
bitrate_average=83060
length=61.936327
playtime=1:01
stream_truncated=false

total_length=61.936327
total_playtime=1:01

*** No problem for test.ogg.

$ ogginfo test-pipe.ogg 
filename=test-pipe.ogg
header_integrity=fail
stream_integrity=fail
stream_truncated=true

serial=1478540987
header_integrity=pass
vendor=Xiphophorus libVorbis I 20011231
version=0
channels=2
rate=44100
bitrate_upper=none
bitrate_nominal=112015
bitrate_lower=none
stream_integrity=pass
bitrate_average=82533
length=61.936327
playtime=1:01
stream_truncated=false

total_length=61.936327
total_playtime=1:01

*** Trouble!

$ ogginfo test-inputpipe.ogg 
filename=test-inputpipe.ogg

serial=33960753
header_integrity=pass
vendor=Xiphophorus libVorbis I 20011231
version=0
channels=2
rate=44100
bitrate_upper=none
bitrate_nominal=112015
bitrate_lower=none
stream_integrity=pass
bitrate_average=83060
length=61.936327
playtime=1:01
stream_truncated=false

total_length=61.936327
total_playtime=1:01

*** No problem.  Now let's try vorbiscomment:

$ vorbiscomment test.ogg 
$ vorbiscomment test-pipe.ogg 
Failed to open file as vorbis: Input is not an Ogg bitstream.
$ vorbiscomment test-inputpipe.ogg
$ 
================================================================

-- System Information
Debian Release: 3.0
Architecture: i386
Kernel: Linux noon.dnsalias.net 2.4.9 #1 sam mar 2 20:48:32 CET 2002 i686
Locale: LANG=fr_FR, LC_CTYPE=fr_FR

Versions of packages vorbis-tools depends on:
ii  libao2                        0.8.2-1    Cross Platform Audio Output Librar
ii  libc6                         2.2.5-4    GNU C Library: Shared libraries an
ii  libcurl2-ssl                  7.9.5-2    Multi-protocol file transfer libra
ii  libogg0                       1.0rc3-1   Ogg Bitstream Library
ii  libvorbis0                    1.0rc3-1   The Vorbis General Audio Compressi