I have shavlik installed and we use more machine groups. These groups contains the computers of which are located in an specific Active Directory OU (per machine group 2 organizational units). But I see that randomly 100 computers are located in an unknown group. I can add these systems to the group where I want to have them but they will still remain in the "unknown" group.
I'm guessing you're talking about how this is displayed in View > Machines. I'd suggest trying to sort this view by the "Domain" column to see if it sorts it better for you. The machine view will sort based on whatever column is first to the left - you can drag any column to this slot.
Let me know if you need further assistance. I hope this helps out.