We recently purchased a 15 year old log home (D log main floor, D log siding on upper floor). On the south wall of the home we have water leaks at the interior beams of the home, where the beams connect to the upper most log. We have caulked the windows, window flashing, the top three logs across the house that includes where the top log meets the log siding and we still experience leaks (primarily in storms from south with wind element). We are on a ridge so driving rain is a common occurrance.
I would recommend having the entire exterior caulked by a professional for starters. Water can come in on one end of the house and run down the logs to the other end of the house before it finds a way inside. It may also require taking the windows out and resetting them properly. Leaks are the hardest thing to find and fix on a log home.