Yeah, there is a lot to learn about stir bars and its not an easy learning curve. I think you are right about it not being lined up. The magnets are likely not 100% coupled so when it changes direction it throws it off balance. The disproportionate weight and buoyancy of my cross bar design probably isn't helping maters. Trial and error is my specialtyReminds me of the MP40s when the magnets arent perfectly lined up. Are they just too weak? Maybe try a slower ramp up speed to see if it will spin?
For the heck of it I stuck a wetside in there. It made a ugly noise so I pulled it out. Not my brightest idea and luckily it was a used spare.