Think about it, a storm that is downstream or on a tributary, (different canyon) isn't gonna be noticed by the upstream guages, right?
There is a LOT of land area and tributaries between the Bailey Guage on the North and the Deckers guage on the South. By the time you get downstream to the confluence at Waterton, a localized storm could easily be (and usually is) the reason for some phantom water appearing between the guages.
"So in two seconds, away we went, a sliding down the river, and it did seem so good to be free again and all by ourselves on the big river and nobody to bother us." -Mark Twain (The Adventures of Huckleberry Finn)