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If you do a new table query of all systems using the assignment path column (aswell as a uninque identifier) can you see the machines at the root?
If so then use this to identify and then move these from root.
As suggested, I have run this query, and there appear to be a large number of machines filed under My Organisation which are invisible in the system view. I can sort them from the query (good thinking, thanks for that), but why can I not see them in System?
I seem to remember that when you move stuff around in directory it tells you (in vague terms) not to drop them into the root as you may not be able to see them again. At least thats what I took the warning to mean.
I just made sure from day 1 not to drop anything in there
They appear to have been dropped there by the domain sync run by a lower level group. Not sure why though. When sorted they all get moved to Lost & Found and become visible.
I also found some duplicate entries, unsure as to why that is too, all of these machines are being brought in from Active Directory where duplicates are not possible. Nor have I enabled the sort which can create duplicates (create here and leave original copy there).