Yeah, leaks are hard to track down, as the place where it is leaking may not be where it is coming in. Leaks can sometimes run quite some distance on the underside of a roof before they drip down.
One more question:
When you talk about resealing the roof, are you talking about the roof joints (or where the air conditioner or vents exit through the roof), or the entire surface of the roof? These are two different projects. Now that we know you have a leak, it is probably a joint that is leaking somewhere. Likely there is no need to reseal the whole roof itself, correct? Is the visible part of the roof membrane in basically good condition, or is it torn or peeling, with fabric showing?