Hi,
I've just posted a patch for 0.04 to the Box Backup web site.
http://www.fluffy.co.uk/boxbackup/
This fixes a bug where calculating changes to big files with lots of
repeated data causes the backup client to use large amounts of memory
and CPU time. It may take so long that the connection to the server
times out, and aborts the backup.
I recommend applying this patch.
Ben