My guess would be that it is something to do with the bedding compound of one or both of the windows. What have you tried so far?
You might try putting some tape around the edge of the windows on the outside temporarily to see if the
leaks stop. I've used the tape used to seal up shrink wrap. If there is exposed bedding compound you might consider waxing or otherwise doing something to prevent the bedding compound from being pulled up when you eventually remove the tape.
Leaks like this are a real pain. It is just as likely that the
water is coming in elsewhere and traveling along a channel.
You might seek out owners of similar
boats if it is any sort of production
boat. If you are having this problem, others likely have as well or may now how to remove the cover and
headliner. If the manufacturer is still around they may be able to help as well.
Good luck,
Harry