I have apache 2 on centos 5x. The webserver is running apache:apache. The website directory is using username:username for file ownership. I always get duplicate sql dumps in the backup. What I find interesting is that people are getting a seemingly random number of duplicated backup files. My backup is getting twelve copies. Here is a log excerpt from the plugin.
142 Temporary Subdirectories copied sucessfully
1479 Temporary Files copied sucessfully
Failed to change backup archive permissions /home/xxx/xxx/wp-content/backup/2008-01-22-11-23-50-full.tar.gz
Archive File created/compressed successfully
It wasn't until I hit the apache_error log when I actually found something:
[Tue Jan 22 11:32:18 2008] [error] [client 65.121.87.229] PHP Fatal error: Allowed memory size of 100663296 bytes exhausted (tried to allocate 59188073 bytes) in /home/xxx/xxx/wp-includes/class-phpmailer.php on line 1110, referer: http://www.xxx.com/wp-admin/admin.php?page=backupwordpress/backupwordpress.php
My max archive to mail me size is 100mb. So I went back in and changed it to 50mb. I still get the same memory overflow above. It looks like calls to class-phpmailer.php are taking an extremely large amount of memory. If I set the archive size to a ridicously small 5mb, the routine doesn't error out but I still get 12 copies in certain directories in the full backup.
When images are uploaded through the wordpress interface it creates a directory called wp-content/uploads. Ownership is given to the default which is apache:apache instead of username:username. These are the only directories that give me trouble. For some reason I haven't been able to track down, each directory has a different number of times each file is duplicated. Some directories have one set of duplicates, some have four, and some have 12.
This leads me to think the duplicates problem is in the tar function. This is also likely where memory hog is as well.