Vent leaks can travel a long way through the roof before being visible. The first thing I'd do is actually remove the vents and AC unit and redo the seals. I found that recaulking only without removing the vents didn't always solve leaks.
By removing the vents, you can reapply caulk between the flange and roof, then caulk the screws before inserting them. This process solved my leaks.
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