I am guessing that some of those small bubbles get sucked into your pump, smashed into smaller bubbles and then pumped into your tank.
If the root cause is bubbles from the weir being pulverized by the pump, perhaps a long piece of open cell foam as a landing for the waterfalliing over the glass would work. I'm thinking the same type of foam used on a skimmer exit pipe- like the one laying between your sump and the middle door.
You may want to keep an eye on something else too, Mike. It's inevitable that at some point in the not too distant future, the clear flex you used will collapse at the bends.
Ahhhhh. That last pic was worth a thousand words. I've always placed baffles so the water must travel under-->over-->under them to move from chamber to chamber. Yours travels over-->under-->over, and crashes down into the return chamber.
If you can take your sump offline a bit, you could just add one more baffle on the return side so the water travels under it to get to the last chamber.
Mike-
Have you ever disassembled your return pump and checked the impeller?
I have had a microbubble problem, only to find several small collinista snails jammed in the impeller. I wouldn't have know they were there if I didn't take the pump apart. The snails were the culprit.