I am using 2011 and I want to have solidworks create a mate folder automatically for each mating part so I can manage the mates better. for some reason it is not doing it but my home system does can you help?
You probably have the View Mates and Dependencies option selected.
Right-click the topmost line in the tree, select Tree Display > View Features
There is a setting for this. On your home computer you have it checked:
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