Why are you backing up Docs & Settings on a Citrix server?
You only need to :
Backup IIS
Backup your Data Store
Backup your Web Interface sites
Backup your Published Applications
http://carlwebster.com/blogs/webster/archive/2008/12/17/Learning-the-Basics-of-XenApp-5-Part-7-of-7.aspxgo down to the bottom of the article.
Since you are using MetaFrame XP, I believe you can use this:
http://www.thomaskoetzing.de/index.php?option=com_content&task=view&id=135&Itemid=207to backup/restore your published apps.