Since you're the one making the dough, and according to your post, you seem to have eliminated the other variables; my guess is that you're using a more active yeast. It could even be the same brand, but fresher or a different batch.
In any case (whether the yeast strain is or is not the cause):
Change your recipe to include a biga or poolish (if you don't already use one or the other) AND an altus. Preferments make the yeast colony more tasty and less active; therefore, smaller bubbles. The altus in particular makes things more consistent. Another benefit, your bread will taste significantly better.
If you use sugar or any other yeast turbo-charger, stop. Or, at least use very, very little.
Use at least three, ten-minute autolyzing (rest after mixing) periods, with French folds between them before kneading. The combination of multiple autolyses and French folds makes slack doughs easier to handle -- if nothing else. However, it should also knock down the number and size of the bubbles formed during the rest period, as well. You didn't want those bubbles anyway. I can tell that you are the sort of master-baking connoiseur who only wants bubbles which form after the knead, when the yeast's had a chance to mature, reflect on its awesome responsibilities, and simmer down a bit.
Make sure you're kneading enough. While chew and not bubble size is the real test, it sounds like your bread might be slightly under-kneaded. I don't care if you're using the world's greatest machine -- don't trust the clock, windowpane. When you get a good windowpane, knead for an extra minute.
Don't trust the clock on proofing times. If it hasn't increased by 90%, it's under proofed (stiff and heavy). If it's increased by more than 110%, it's over-proofed (flaccid and gassy -> big bubbles). "Doubling" is the ideal. The exception to the doubling rule is the final proof after formation and before baking. Only take a 2/3 rise there, to allow for some oven spring -- even with focaccia.
If you can find the way to afford the time (even if it means starting a day earlier and retarding the final proof in the cooler), add an extra rise. Three rise is the way to go. Let the yeast spores move through their life cycle as the colony uses up the food. Slightly tired, stressed yeast makes for better taste and texture. A retarded rise also allows the weight of the dough to press the down down and collapse large holes.
Change your punch down technique, whether it's total violent deflation or gentle "pull down" to French fold. Changing to French fold has been a big positive for all aspects of crumb structure in my baking.
After formation, halfway through the final proof, turn your loaves over. The turn will partially deflate and add some extra time (I guess I'm not your best friend regarding time). The principle is the same, "weight pressing down" as in the retarded rise suggestion, but applied even more directly. Ideally, the last rise will be retarded and include the turn.