This is just a guess, but I'm going to say you do NOT want the diffuser completely submerged. The whole point of the diffuser is to stop those little bubbles from getting into the aquarium, and if it is submerged, those bubbles can just flow right out the top and into the aquarium. The idea is to have those bubbles flow through the sponges before they get into the aquarium water.
I've noticed the same thing, that the bubble flow isn't perfectly constant, but it hasn't been a huge deal for me...
38 Gallon (Freshwater): 1 Green Swordtail, 3 Yo-Yo Loaches, 1 Clown Pleco, 1 Blue Gourami, 4 Otocinclus, 7 Cherry Barbs.
46 Gallon (Saltwater): 60 pounds Lalo Live Rock, 60 pounds aragonite sand, 1 Coral Beauty Angelfish, 1 Peppermint Shrimp, 1 Mushroom Coral, 1 Emerald Crab, various snails and hermit crabs.
10 Gallon (Saltwater quarantine):