I've set up a Smart Group, which displays the correct Macbooks when viewed in the dashboard. However, when I use the Smart Group as a Scope Target for configuration profiles, with Specific Computers and All Users selected, I get a different set of Macbooks that fall in scope of the profile. It also seems to be a little random i.e. I have 266 computers in the Smart Group, but have a profile with 95 computers and others with upto and over 300.
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It would be kind of pain in the neck, but I wonder what would happen if you made a new Smart Group with a name that's not even similar to another smart group you have. It sounds like you're looking at two different Smart Groups, which shouldn't be the case I realize, but I might take a handful of the computers and make a new Smart Group and start adding to that a few at a time.