I have an RDS collection using 2012 R2 licence server with Per Device licences installed. All clients are Windows 7. Some clients have been allocated a licence and keep this licence assigned until it expires.
Other desktops get assigned a licence, each time they use a remoteapp, so in the issued licence list from WMI, they have multiple assigned licences all of which are active. The desktop HWID is the same, the only thing I notice is that the licences are IssuedTo to SYSTEM account but in the cases where the licences are assigned correctly, they are IssuedTo a named user in the domain. Example below (apologies would not allow me to paste screenshot):
ExpirationDate IssueDate LicenseId LicenseStatus sHardwareId sIssuedToComputer sIssuedToUser
20160724154156 20160520114224 11089 2 0002012265bfe99f86d9228bb814801b7dd0 DESKTOP-02 ADUSER1
20160629233135 20160201134902 6206 2 000201b69c8a45fd9de55288ef3291fd6a35 DESKTOP-03 ADUSER3
20160607115219 20160309115219 7956 1 000202095bfa82934dff11ae2d026f259350 DESKTOP-04 SYSTEM
20160724114356 20160425114356 10100 1 000202095bfa82934dff11ae2d026f259350 DESKTOP-04 SYSTEM
20160726113149 20160427113149 10221 1 000202095bfa82934dff11ae2d026f259350 DESKTOP-04 SYSTEM
20160727115821 20160428115821 10272 1 000202095bfa82934dff11ae2d026f259350 DESKTOP-04 SYSTEM
20160811083350 20160513083350 10797 1 000202095bfa82934dff11ae2d026f259350 DESKTOP-04 SYSTEM
20160714063330 20160429080538 10302 2 000202095bfa82934dff11ae2d026f259350 DESKTOP-04 SYSTEM
20160823164146 20160531114215 11476 2 000202095bfa82934dff11ae2d026f259350 DESKTOP-04 SYSTEM
20160607092024 20160411091328 9399 2 000203285cb65a8349658370d0524c02ee88 DESKTOP-05 ADUSER2
20160706113908 20160407113908 9298 1 00020331150560d05c654282885379c9843d DESKTOP-06 SYSTEM
20160706142006 20160407142006 9306 1 00020331150560d05c654282885379c9843d DESKTOP-06 SYSTEM
20160713074701 20160414074701 9601 1 00020331150560d05c654282885379c9843d DESKTOP-06 SYSTEM
20160714080745 20160415080745 9673 1 00020331150560d05c654282885379c9843d DESKTOP-06 SYSTEM
I think this might be permissions related, have read about licensing requiring AD attribute changes but that seems to only be for per user licences