Hi,
I had a SeaClone sometime ago... Like most simmers, the production of foam is variable. The older the tank, the more predictable the skimmer is.
Is your skimmer still foamless? A few days of no foam is normal... Also, sea clone skimmers have a very bad habit of needing constant adjustments. Maybe it needs readjustments...
I doubt that switching substrate had any effects in terms of nutrient load, while in fact it should have increase the nutrient load because by disturbing the bottom of the tank you should have re-suspended some of the organic matter that was "locked" in the layers deep down in the tank.
One more thing comes to my mind BTW... Did you perfom any MAJOR water change when you switch substrates??? The chelating agent in the anti-chlor can affect the stability of the bubbles in the skimmer...
As you can see, not an easy question to answer.
HTH