This issue has been fixed. See ITMS 7.6 HF3 (DOC8873
A workaround is available for those that can't upgrade: it is to add those missing Filters as inclusions.
Note: You could edit the XML for that filter and add the desired Filters (since the AD Import Filters are not editable directly).
Basically add the following into the XML for the desired master Security Group- Users to Machines and import it back: