MC's Ogg Vorbis encoder is based on the reference Xiph Vorbis library. During the MC11.1 development cycle I asked if the well-known aoTuV beta 4.51 encoder could be used, but I suppose JRiver wanted to use the "official" library.
As far as I know the MC encoded Ogg Vorbis files should be fine.
Did you try to encode two otherwise identical test files? I mean: using the same source, the same encoding options, the same tags, the same latest MC version, just with a different oggenc.exe file in the plugins folder.
Unlike many other programs MC can add cover art to Vorbis tags. That is unofficial and can be incompatible. For example, Tag&Rename cannot handle such files. Do you happen to use embedded cover art?
EDIT
This quote is from the post in which I asked for the aoTuV version:
Ogg Vorbis
11.1.123 (02/16/06)
13. NEW: Updated Ogg Vorbis encoder to version 2.8 (libvorbis version 1.1.2)
Thanks for this too!
However, I am curious why you chose this version (Oggenc2.8 using libVorbis v1.1.2 with IMPULSE_TRIGGER_PROFILE Option 2005-12-08) instead of the aoTuV b4.51 version (Oggenc2.8 using aoTuVb4.51 2005-12-08) ?
from: http://www.hydrogenaudio.org/forums/index.php?showtopic=39546&view=findpost&p=348793
Q: Sorry I think I missed something... libvorbis is now 1.1.2 ? how does it relate to aoTuVb4.51 ?
A: libvorbis 1.1.2 is the official Vorbis library coming out from Xiph.Org that is mostly based on the old aoTuV beta 2. aoTuV beta 4.5 is Aoyumi's tuned version of libvorbis (based on libvorbis 1.1.1).
Aoyumi has developed his Vorbis encoder version about two years after the beta 2 version. Beta 4.51 is the much praised test winner.
EDIT
The encoder differences are explained further in that HA thread.