That's strange. It seems to be ok here, using the OGGENC available on the MO3 page. What format was the source you tried, eg. sample rate and channels?
Source file was just a standard wav file as ripped from a CD with EAC, 44.1/16/2.
(Trying some more, changing oggenc version doesn't seem to do much, usually I'm using the optimized one I've linked to above.)
Just to be sure, your command-line is this?
oggenc -t %1 -a %2 -l %3 -d %4 -N %5 -G %6 -c %7 -o %o -
Does the source file have any tags? If so, you could try removing those from the command-line, in case they're the problem.
oggenc -o %o -
No. Ordinary WAV, no tags. No changes with that line.
If that still doesn't work, you could also try this.
oggenc -o %o %i
Yes, that changes stuff, so also this line works with all encoders:
oggenc -q 5 -t %1 -a %2 -l %3 -d %4 -N %5 -G %6 -c %7 -o %o %i
Meaning that problem is encoding from stdin
.... Well, other frontends, e.g. foobar2000 don't have a problem with oggenc doing that..... Any clues?