Puffer? Crushed coral? Messy eater. What else is in there? Sounds like a problem with nasty water may perpetuate.
I'd be alittle suspicious also of a 220g skimmer on a 90g tank. I'm not sure, but the water might move too fast thru that to really help. Maybe a 125g rated skimmer??
What are your nitrates reading bythe way?
Any other thoughts on that big skimmer from anyone that might not be guessing like me??