The desktop.ini files in the locations you indicate should have been
restored with the "hidden" attribute set.   As Andy Raibeck indicated
there's an APAR in the works for that problem. You don't need to delete
the files.  You can hide the files again via attrib +h or the properties
tab of the explorer window when displaying the file properties.

For example say desktop.ini for "all users" start menu resides in
C:\Documents and Settings\All Users\Start Menu, Open a command prompt
window, change directory to this directory and issue attrib +h
desktop.ini.  Same action needed for  C:\Documents and Settings\All
Users\Start Menu\Programs, and C:\Documents and Settings\All Users\Start
Menu\Programs\Startup.  If this is happening for a specific user you may
need to perform the same action for C:\Documents and Settings\<user
name>\Start Menu\<etc>.

Regards,

Mike Dile
Tivoli Storage Manager Client Development
Tivoli Software, IBM Software Group
mikedile AT us.ibm DOT com