Problem: the repair person used corrosive flashing as a bib. When nail heads are covered by flashing that will rust, eventually it does get rusty and the exposed nail head, even though tucked down in the slot, will leak.
Solution: Use your ripper to redo the corrected flashing and replace it with copper or painted aluminum or other non-corrodible bib material. When using painted aluminum, use a brown color and leave the brown facing out.
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Problem: the repair person didn’t cover the nail in the slot with any piece of bib flashing. It’s not uncommon for a rooter to replace a slate, nail it in the overlying slot like he should, then leave it like that without covering the nail with flashing, as if his brain was working fine and then just shut down before the job could he finished. This is one of the hardest hidden leaks to find, because the nail is tucked in right at the top of the slot where it’s hardest to see, especially from above, which is the most common vantage point for a roofing contractor. Then the repair nail rusts away until it matches the color of the roof and becomes invisible.
Solution: When examining the leaking area, always look in the slots for hidden nails. Look closely.