I am not familar with the whole "Jaubert" thing but i know the idea behind the plenum system. i've seen one setup like that in a 2000Gal tank.
I'm thinking, using crushed corals could defeat the purpose of having a "VOID" place for bacteria, so you might wanna check into that.
Obviously, without proper maintenance for quite sometime, would result in too much nutrient (NO3 & PO4) build-up, thus ALGAE. I hope that you just siphoned the surface of the sand and not "VACUUM" the sand, as vacuuming MIGHT reset your VOID inside the plenum, releasing toxic substances/gases into the water column. I also hope you changed a considerable amount of water, slow and gradual.
Your clown could have had marine velvet, or brookynella, or oodinium, or cryptocaryon. i'm just guessing here, but all those have the symptoms you are describing. Meth blue in QT for a week or two worked wonders for me againts those diseases.
to finish...
Maybe it's time to teach your kid how to handle a bucket, for water changes when you are away, hehe.
Please provide us with water test results for us to help you better. if you do not own one or could not borrow one.... help yourself by getting a hold of test kits. Test kits are a matter of life, death and algae, i always say. Test kits for NH3/NH4, NO2, NO3, PO4, KH, PH, CA, Mg.
Please provide us with some more details of your setup. Pictures would be AWESOME!
Invest on a good lighting system since you are keeping photosynthetic sessile invertebrates as well, they will thank you for it.
Good luck and happy reefing man!