We ran into the exact same problem yesterday and engaged Cisco support. The technician referred to it as a VMware bug in the update that changes the UUID of the host. From my understanding, previous versions of ESXi were incorrectly reporting the UUID of the host. Updating to Update 2 fixes that bug and causes the host to report a different, correct UUID to the 1000v. The 1000v sees it as a new host and tries to allocate a license to it, but the old UUIDs are still hogging up the licenses. The technician did say that later versions of the 1000v have a different licensing structure that does not refer to the host UUID. I have a ticket in with VMware to see if they have a way to mitigate this issue. In the mean time, I'm not updating any other hosts to Update 2.
From the Resolved Issues list in the Update 2 Release Notes: http://www.vmware.com/support/vsphere5/doc/vsp_esxi50_u2_rel_notes.html
