Dennis - I think these are a couple of interesting and in some ways interrelated points. I definitely think you might be on to something here in questioning the water source for the tropical reef tank for a few reasons including the issue of possible contaminants, salinity fluxuations (can't remember if you adjust this or not), "inappropriate flora/fauna die off, and general organics levels. Obviously it would be more work but using RO/DI with a consistent salt mix might be a better approach. In which case... I would definitely think about adding the refugium to help establish a population of more appropriate micro flora/fauna. That could be jump started with some donations for existing systems. In combination with the other suggestions re circulation, skimming etc., I think you would be in pretty good shape.