The administrator (AD) user, with a role that has all the privileges for a DSM user, is assigned in a particular cluster. From the vSphere console, this user can view all the accessible virtual machines and folders. After a synchronization, the DSM does not display the machines that should be in the folder. This issue happens with Deep Security Manager 9.5 SP1 Build 5623 in vCenter 5.1.
The issue occurs because vCenter 5.1 Build 799731 is incompatible with DSM 9.0 and 9.5.
To resolve the issue, upgrade to vCenter 5.1 Update 3 or vCenter 5.5.