SQL Server 2005: Integration Services Stored Packages is empty. Why?
The packages themselves are stored in the msdb sysdtspackaes90 table. 


  It’s important to note that the SSIS
  server isn’t aware of packages stored
  in the File System until those
  packages have been imported to the
  File System folder in the SSIS
  service.


... 


  While the SQL Server Management Studio
  is shipped using the default folder
  locations of MSDB and File System, you
  can freely add new folders to this
  structure using the Create New Folder
  option. When you create a new folder
  beneath the File System system folder,
  a new directory will be created in the
  file system. By default, these
  directories are located in the
  c:\Program Files\SQL
  Server\90\Packages directory.
  Importing packages to a File System
  folder will result in the package
  being copied to the like named
  directory in the file system. For
  folders that are created under the
  MSDB folder, a new entry is added to
  the sysdtspackackefolder90 table that
  tracks the folder structure. However,
  it’s important to realize that the
  packages themselves are still stored
  in the msdb sysdtspackaes90 table. The
  Folders option in the SQL Server
  Management Studio essentially gives
  you a way to apply and organization
  structure to your packages, enabling
  you to group like packages together.


Managing and Deploying SQL Server Integration Services

Anyway, I recommend to install all SPs.