Some recommended FLAC/Vorbis tags are listed here:
http://www.xiph.org/vorbis/doc/v-comment.html, but unfortunately the Album Artist and Disc Number fields are not included and the tag mappings may vary from a program to another.
Media Jukebox reads and writes:
DISC #ALBUM ARTISTdBpoweramp writes (at least by default, I don't know if it allows to tweak the tag mappings):
DISCNUMBERALBUMARTISTYou would need to create the DISCNUMBER and ALBUMARTIST user fields in MJ, update the library data from file tags, and inside MJ copy the field values to the correct fields (this is actually quite easy and fast, you can process all files at the same time).
Another option would be to buy Media Center 15. It has some FLAC tagging changes that improve compatibility with many other programs and devices.
MC15 reads:
DISC # and
DISCNUMBERALBUM ARTIST and
ALBUMARTISTMC15 writes:
DISCNUMBERALBUM ARTIST and
ALBUMARTISTI don't know if JRiver has plans to implement these changes in Media Jukebox.