<pre><code>rsync -auve ssh --backup --suffix='2008-10-03-1514539' --backup-dir='/tmp/' module.pm root@web1:/path/to/module.pm
</code></pre>

<p>I run this command without the --backup-dir option and when it copies the file over, it creates a backup with a current timestamp. When I include the --backup-dir option, it makes the backup into the /tmp/ directory but never attaches my suffix. </p>

<p>There is nothing in the <a href="http://samba.anu.edu.au/ftp/rsync/rsync.html" rel="nofollow noreferrer">manual</a> to suggest that you can't use both these options together. I've played around with the order also and nothing seems to fix it.</p>

<p>Does anyone have a solution to this?</p>

the manual says:
--backup                make backups (see --suffix & --backup-dir)
--backup-dir=DIR        make backups into hierarchy based in DIR
--suffix=SUFFIX         backup suffix (default ~ w/o --backup-dir)
so it seems that you can use one or the other, not both (as I guess you want a way to determine what's a backup you use a suffix or a directory).
As a way to fix this, why don't you keep the suffix and modify the destination to include the backup directory.