We have had similar issues at the Praetorians. There have been two main solutions:
Henry has cut off the pins, drilled out the holes a little so the stems then go fully into the holes.
I on the other hand have removed the stems completely, and replaced them with golf tees. I remove the point of the golf tee, stick the ball holding end to the base. Drill a small hole in the top of the golf tee where the point was and put a magnet on the base of the model. This worked extremely well on my 2 Destroyer Lords, 9 Heavy Destroyers, 15 Destroyers and 3 Canoptek Spyders. (Unfortunately I dont use my crons much now cos they are a little rubbish now!)