What stacking software are you using? Some programs have a planetary mode that aligns on the planet itself, not the whole frame, which might help keep the moons from getting smeared.
Stacking images without blurring details sounds ideal, but that method can mess up planetary shots. Aligning multiple frames often smears the fine lines on Jupiter and makes the moons look fuzzy. I've seen stacked photos where the planet's bands get all soft and lose definition. Honestly, just picking your sharpest single image and tweaking the contrast usually works better.