Did you quarantine the fish before you added it with the rest? The Shubie could just be reacting to stress, but if probably wouldn't hurt to take it out and quarantine it for a few weeks -- if the fish has a disease or parasites, the added stress of a new environement could be making it sick. At least it would give the Shubie a chance to rest and adjust. But if it was already carrying something, the rest of your fish have been exposed, so be sure to keep a close eye on them, as well.
How large is your pond, and when you say "large koi," how big are they? What kind of filtration & aeration are you using, and what have your temperatures been running [better yet, if you check the temp of your water.].
We really like to see the actual numbers that you get when you check your water parameters. The numbers offer more information when there is a potential problem to solve. And I don't know that much about koi ponds to know the significance of checking salinity, but personally I'm of the opinion that salt should only be used as a therapeutic treatment and not added to the pond -- koi and goldfish are freshwater fish. But someone will correct me here if I'm wrong about this -- just my opinion [I don't mean, correct me if I'm wrong about koi being freshwater fish, but the part about adding salt routinely...]