This morning I woke up to find water in the bottom of our chimney. We have no fire, the gas cowl is still in place, the flaunching and flashing are quite new. It's a metal cowl that is a cylinder with horizontal slots. I looked up into the fire place and can see water in the ledge at the bend and I'm firmly sure I saw a drop come down from above onto that ledge. I can't see anything else inside the house and having seen the drip come down it seems to be inside the fireplace. The amount of water at the bottom is quite small, about a spoonful. Any ideas what I need to check?
As long as your chimney cap (I assume that's what you describe as a 'cowl'?) is in place, you are probably fine.
Although chimney caps are designed to keep out rain and critters, they can't fight the occasional sideways rain drop. The little amount of water that enters the chimney from those atmospheric anomalies won't hurt a thing. Short of completely blocking off the chimney with a weathertight cap (not possible if you use it with gas appliances, as you stated), just keep truckin.