I'm having the same problem.  I'm using Evolution 3.6.4 under Ubuntu Raring 13.04 (amd64).

If I watch a backup from GDB, this is what I observe:

process 30858 is executing new program: /usr/lib/evolution/3.6/evolution-backup
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New Thread 0x7fffe9b6f700 (LWP 31032)]
[New Thread 0x7fffd2d7f700 (LWP 31033)]
** Message: evolution --quit
** Message: rm /home/kip/.local/share/evolution/.running
rm: cannot remove ‘/home/kip/.local/share/evolution/.running’: No such file or directory
** Message: dconf dump /org/gnome/evolution-data-server/ >/home/kip/.local/share/evolution/backup-restore-dconf-eds.ini
** Message: dconf dump /org/gnome/evolution/ >/home/kip/.local/share/evolution/backup-restore-dconf-evo.ini
** Message: cd /home/kip && tar chf - .local/share/evolution .config/evolution evolution.dir | gzip > '/media/kip/Kip-3TB/Mail/evolution-backup-20130517.tar.gz'
** Message: rm /home/kip/evolution.dir
[Thread 0x7fffd2d7f700 (LWP 31033) exited]
[Thread 0x7fffe9b6f700 (LWP 31032) exited]
[Inferior 1 (process 30858) exited normally]

However, the backup is, as the OP reported, way too small.

$ du -hs evolution-backup-20130517.tar.gz 
968K	evolution-backup-20130517.tar.gz

If I look inside the archive it generated, ignoring configuration files, and just look at everything else. There's not much, if any, mail.

$ find evolution-backup-20130517/ | grep -v config
evolution-backup-20130517/
evolution-backup-20130517/.local
evolution-backup-20130517/.local/share
evolution-backup-20130517/.local/share/evolution
evolution-backup-20130517/.local/share/evolution/calendar
evolution-backup-20130517/.local/share/evolution/calendar/system
evolution-backup-20130517/.local/share/evolution/calendar/system/calendar.ics
evolution-backup-20130517/.local/share/evolution/calendar/trash
evolution-backup-20130517/.local/share/evolution/datetime-formats.ini
evolution-backup-20130517/.local/share/evolution/printing.ini
evolution-backup-20130517/.local/share/evolution/tasks
evolution-backup-20130517/.local/share/evolution/tasks/system
evolution-backup-20130517/.local/share/evolution/tasks/system/tasks.ics
evolution-backup-20130517/.local/share/evolution/tasks/trash
evolution-backup-20130517/.local/share/evolution/signatures
evolution-backup-20130517/.local/share/evolution/camel-cert.db
evolution-backup-20130517/.local/share/evolution/backup-restore-dconf-eds.ini
evolution-backup-20130517/.local/share/evolution/addressbook
evolution-backup-20130517/.local/share/evolution/addressbook/system
evolution-backup-20130517/.local/share/evolution/addressbook/system/log.0000000001
evolution-backup-20130517/.local/share/evolution/addressbook/system/addressbook.db.summary
evolution-backup-20130517/.local/share/evolution/addressbook/system/photos
evolution-backup-20130517/.local/share/evolution/addressbook/system/addressbook.db
evolution-backup-20130517/.local/share/evolution/addressbook/system/contacts.db
evolution-backup-20130517/.local/share/evolution/addressbook/trash
evolution-backup-20130517/.local/share/evolution/categories.xml
evolution-backup-20130517/.local/share/evolution/backup-restore-dconf-evo.ini
evolution-backup-20130517/.local/share/evolution/backup-restore-gconf.xml
evolution-backup-20130517/.local/share/evolution/memos
evolution-backup-20130517/.local/share/evolution/memos/system
evolution-backup-20130517/.local/share/evolution/memos/system/journal.ics
evolution-backup-20130517/.local/share/evolution/memos/trash
evolution-backup-20130517/.local/share/evolution/mail
evolution-backup-20130517/.local/share/evolution/mail/1260670856.2904.2@kip-laptop
evolution-backup-20130517/.local/share/evolution/mail/vfolder
evolution-backup-20130517/.local/share/evolution/mail/vfolder/UNMATCHED.cmeta
evolution-backup-20130517/.local/share/evolution/mail/vfolder/folders.db
evolution-backup-20130517/.local/share/evolution/mail/local
evolution-backup-20130517/.local/share/evolution/mail/local/.Templates
evolution-backup-20130517/.local/share/evolution/mail/local/.Templates/cur
evolution-backup-20130517/.local/share/evolution/mail/local/.Templates/cur/1367821451.2646_0.rommel:2,DS
evolution-backup-20130517/.local/share/evolution/mail/local/.Templates/tmp
evolution-backup-20130517/.local/share/evolution/mail/local/.Templates/new
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts.cmeta
evolution-backup-20130517/.local/share/evolution/mail/local/.Outbox.ibex.index.data
evolution-backup-20130517/.local/share/evolution/mail/local/.Outbox.cmeta
evolution-backup-20130517/.local/share/evolution/mail/local/..#evolution.Junk.cmeta
evolution-backup-20130517/.local/share/evolution/mail/local/..cmeta
evolution-backup-20130517/.local/share/evolution/mail/local/cur
evolution-backup-20130517/.local/share/evolution/mail/local/.Sent
evolution-backup-20130517/.local/share/evolution/mail/local/.Sent/cur
evolution-backup-20130517/.local/share/evolution/mail/local/.Sent/tmp
evolution-backup-20130517/.local/share/evolution/mail/local/.Sent/new
evolution-backup-20130517/.local/share/evolution/mail/local/.Templates.cmeta
evolution-backup-20130517/.local/share/evolution/mail/local/tmp
evolution-backup-20130517/.local/share/evolution/mail/local/.Outbox.ibex.index
evolution-backup-20130517/.local/share/evolution/mail/local/.Sent.cmeta
evolution-backup-20130517/.local/share/evolution/mail/local/.Outbox
evolution-backup-20130517/.local/share/evolution/mail/local/.Outbox/cur
evolution-backup-20130517/.local/share/evolution/mail/local/.Outbox/tmp
evolution-backup-20130517/.local/share/evolution/mail/local/.Outbox/new
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368742305.2680_381.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368742119.2680_380.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368227220.2641_368.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368655085.8489_372.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368654878.8489_370.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368229225.2641_369.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368663016.8489_376.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368662035.8489_374.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368424023.2647_370.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368663161.8489_377.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368654893.8489_371.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368661903.8489_373.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368662109.8489_375.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368665974.8489_378.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368829633.7880_382.rommel:2,DS
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/cur/1368667214.2680_379.rommel:2,DST
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/tmp
evolution-backup-20130517/.local/share/evolution/mail/local/.Drafts/new
evolution-backup-20130517/.local/share/evolution/mail/local/folders.db
evolution-backup-20130517/.local/share/evolution/mail/local/..maildir++
evolution-backup-20130517/.local/share/evolution/mail/local/..#evolution.Trash.cmeta
evolution-backup-20130517/.local/share/evolution/mail/local/new
evolution-backup-20130517/.local/share/evolution/mail/trash
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Templates.ibex.index
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Templates
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Templates.ibex.index.data
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Outbox.cmeta
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Sent.cmeta
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Sent.ibex.index
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Drafts.ibex.index
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Drafts
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Outbox.ibex.index.data
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Drafts.cmeta
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Inbox.ibex.index.data
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/.#evolution.sbd
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/.#evolution.sbd/Junk.cmeta
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/.#evolution.sbd/Trash.cmeta
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Templates.cmeta
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Sent.ibex.index.data
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Drafts.ibex.index.data
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Sent
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Inbox.ibex.index
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Inbox.cmeta
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Outbox
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Outbox.ibex.index
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/folders.db
evolution-backup-20130517/.local/share/evolution/mail/trash/local_mbox/Inbox
evolution-backup-20130517/.local/share/evolution/mail/trash/emae-check-authtype-0x7c8a670
evolution-backup-20130517/.local/share/evolution/mail/trash/emae-check-authtype-0x7c8a670/folders.db
evolution-backup-20130517/.local/share/evolution/mail/trash/imapx
evolution-backup-20130517/evolution.dir