If I'm going to write a blog about caulk, I need to get something out of the way first; it's pronounced kawk, not kallllk. The "L" is silent, and the word rhymes with walk or talk. If you're uncomfortable uttering this word aloud, try 'sealant' instead. Moving on.
As we learned from Charles Buelle's blog about caulking not caulking at the base of tiled shower walls, there are just some places where caulking doesn't belong.
One of the most common offenders is at the bottom of storm windows; if the base of the storm window gets caulked shut, where does the water go?
Nowhere. It just sits there and rots the window out. Most storm windows already come with weep holes in the bottom of the window to allow water to drain out; keep these holes open.
When I find caulking at the base of storm windows, I recommend repair. The fix can be as simple as drilling a bunch of holes at the base of the storm window.
Reuben Saltzman, Structure Tech Home Inspections