Another question occurred to me this morning that I haven't…

The good news is that you are aware of the leak and the area.  Unfortunately - it would be extremely difficult to give an accurate assessment of what's causing the issue.   If I was performing the home inspection and noticed the staining, my first thoughts would be we have a roof leak, it could be a torn shingle, popup nail head, hail damage or even flashing damage.  Other possible causes of leaks are ice damming (but due to the time of year you see it - probably not the cause), condensation from an exhaust vent (bath or kitchen), and even animal excretions.

Hiring a home inspector or looking for a roofing contractor to investigate further would be my best advice.  Even if the area goes unnoticed for years, the cause most likely didn't fix itself and the damage could still be occurring outside of your sight.  Costs should be minimal for a specific evaluation (some roofing contractors would be free).

Hope that helps - and if you do have them investigate I'd like to know the outcome.

Thanks for asking for me - William

I'm happy they were able to determine the point of the leak.  Make note of the area as you'll want to monitor it in the future, even with the sealant reapplied, it can become less affective over time.  Sun, Rain and other weather can lessen the life span of the sealant just like other roofing components.  Thank you for using Just Answers and allowing me to assist. Have a wonderful day.  Also, customer service can direct any future inquiry to me if you would like my help again  - William