That screenshot you sent is of convo view, which doesn't show folders unless you expand/open.

-If you expand the arrows on the left to see the hybrid view, solo items still don't show folders, that's a bug/RFE somewhere:

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Contradictory point: Though that might not be your problem as the zimbraPrefGroupMailBy on most of the 'HAS issue' accounts are already set to message view - unless they've changed since reporting the problem to you.
I didn't see any zmprov ga
user@domain.com output with the new zimbraPrefListViewColumns that was added to 5.0.9 so I don't think that's a lead (it's an implicit setting that's set on first logout/session end if they've adjusted the columns visible).
Assuming it's not just the convo vs message view - let us know if it's solved in a 5.0.10 upgrade of if it persists.