I have the same problem and would love some insight from someone that may know what is up with this.
I drove 6 hours yesterday through rain and storms all day, seriously tons of water, rivers flooded and everything...
Not one problem with the jeep at all. Took in the cool air and loved every minute of the ride.
Now, on the other hand, three days ago I splash through a puddle on my road and she starts spitting and sputtering into the driveway. Starts back up after lunch, sputters when backing out, cuts out on me for a second or two then picked back up for the ride.
Its wierd that I can drive in heavy rains without an issue, but I splash in a little puddle and she cuts out on me.
Im wondering if water puddles up on the battery and shorts it for a few??? I also thought about spraying silicon on all my connections under the hood.