dumb question: did you rinse the flourite and the gravel really good beforehand? bacterial blooms has never been my problem in my years of fishkeeping though.
Totally off topic but I was just wondering why you went the refugium route? Won't the whole sump setup offgas alot of the Co2? Although I like the " tank under a tank " look. Under the stand is not a good viewing location IMO, just my two cents.