We use controller software version 12.8 when configuring machines for sites. Since updating to 5.2, all machines have disappeared except for four - two of those were configured as version 12.0 and two were configured as version 12.4.
When I select to create a new machine in the controller manager, version 12.8 is no longer an option and I suspect this is the reason most of our machines no longer appear in the assignment lists.