Sorry you had no takers on your question. I'm not an expert on windows, either, but here are a few things you might consider.
First, it's not clear if you're only talking about caulking around the window frames, or also sealing the window glass into the frames.
There are a number of reasons why water might enter on the top inside of the window. An inspection of the attic/crawl space should be sufficient to determine if it is a roof problem (if there is no crawl space above the ceiling, a roof leak is not likely unless there is other evidence of a leak).
If the roof is OK, check the outside of each leaking window at the upper edge, and also above it. Even a narrow crack can draw water in--in fact, in some cases a narrow crack can draw more water in than a wide one, due to capillary action!
Make sure the crack is clean and dry before applying new caulking--the number one cause of caulking failure is improper surface prep!