I recently started having this issue around the time that my primer magazine tip broke. For around 1/10 primers, the primer will drop onto the shuttle or, worse, fling forward from the press and onto the floor. After the tip broke I replaced it with a new one. Since then, I've checked the height of the primer cup, and made sure that the primer cup travels all the way and stops directly underneath the primer magazine.
The only thing I can see that might be wrong is that the primer cup is slightly bent, and sitting slightly off.
Has anyone else done successful troubleshooting on this issue?