Using --link-dest works on small directory tree but not large one

[Robot Robot]

I'm using version 2.6.3 on OS X. I'm trying to use --link-dest to keep some rolling backups of production websites. There is about 2GB of data in 60,000 total files. I do an initial rsync to get an initial copy of the data, and each day thereafter I run rsync again with --link-dest to create a new daily backup. For some reason, in the subsequent runs, rsync updates a whole lot of files that haven't changed at all. The files in the source and in the link-dest location have identical contents, are the same size, and have the same modified date. I can't seem to find any patterns in the files it decides to bring back down the subsequent times. Sometimes it will bring down the entire directory tree again, and sometimes it will bring down slightly less than the whole tree.

I've tried running the same commands on subsets of the directory tree, and everything works perfectly. The problem only appears when I try to sync my entire directory tree.

This is what I'm doing:

$ rsync -vv --progress --archive --compress --numeric-ids --delete -e ssh [EMAIL PROTECTED]:/usr/home/blah/websites/ /backup/websites/1
$ rsync -vv --progress --archive --compress --numeric-ids --delete --link-dest=../1 -e ssh [EMAIL PROTECTED]:/usr/home/blah/websites/ /backup/websites/2
$ du -hsc /backup/websites/*
2.1G    /backup/websites/1
2.1G    /backup/websites/2
4.2G    total

If, however, I run the following, it all seems to work perfectly:

$ rsync -vv --progress --archive --compress --numeric-ids --delete -e ssh [EMAIL PROTECTED]:/usr/home/blah/websites/site1.com /backup/websites/1
$ rsync -vv --progress --archive --compress --numeric-ids --delete --link-dest=../1 -e ssh [EMAIL PROTECTED]:/usr/home/blah/websites/site1.com /backup/websites/2
$ du -hsc /backup/websites/*
35M    /backup/websites/1
0    /backup/websites/2
35M    total

This is frustrating to debug because there's a lot of data being transferred, and it only occurs when I try to sync the full tree. Is this a bug? Am I doing something completely wrong and stupid? I'm happy to provide more detailed info if you need it. Thanks!!

-- 
To unsubscribe or change options: https://lists.samba.org/mailman/listinfo/rsync
Before posting, read: http://www.catb.org/~esr/faqs/smart-questions.html