It sounds like your composer setup is mucked up, and it may have issues talking to the database or vCenter. I'm not sure that there is an easy way to recover from this and get everything working again.
When using linked clone pools, information about desktops is stored in three places - vCenter, the View LDAP database, and a database used by Composer. The (Missing) error next to new desktops means that the desktop is in the View LDAP database but can't be found in vCenter,. They may not be showing up in the Composer database either.
The user account that you use to log into View Administrator doesn't need to have any special rights in Active Directory. View Composer should be running as a domain service account with local admin rights on the server. It should not have domain admin rights. Composer can be set up to use other accounts to handle QuickPrep tasks - those accounts need to have very specific rights in Active Directory and vCenter. More information on those permissions can be found here: http://seanmassey.net/2014/01/06/horizon-view-5-3-part-4-active-directory-and-vcenter-configuration/
