First, make sure that the short pipe is indeed running a full siphon and no new bubbles or air is entering it. If you are still getting bubbles I might know the solution.
So I actually had this issue with my bean animal when I set up my tank about a week ago. I knew everything was set right to work with no bubbles but even after 2 days of running the bubbles wouldn't disappear out of my main drain. The only reason I could come up with was that there was a leak somewhere letting bubbles enter but I saw no leak. Then it occurred to me that if bubbles are entering the pipes then the leak won't show when it's under siphon because of the pressure. So I let my drain run fully open and there it was, a tiny leak in one of the joints letting small amounts of air in. Patched it up and the bubbles were instantly gone. Give it a try.
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