I had the same problem on my KZ. The window openings are oversized, the window being held in place with compression. This leaves a gap beneath the window. Over time the bouncing/vibrations of road travel take their toll, and the window shifts downward. This leads to small gaps on the top corners where water can intrude.
My solution was to shim the window up using some PVC trim that custom cut to fit. Be sure not to shim it so it's centered in the opening. This will prevent future sagging of the window. Nothing more than butyl tape is needed.
I would also inspect your other windows. If a window has sagged the butyl tape will leave a trace of it above the window. If you see this I'd go ahead and reset the window.
