I am assuming you are aware Bernina bobbins are specific to machines. You can't slap any old bobbin in the machine. And even different Bernina models take different Bernina bobbins. Also Bernina's need to have the thread feed a specific way. Once you put the bobbin in the bobbin case pull the thread and ensure that the bobbin is rotating clockwise. Have you noticed if your machine is having problems with only one specific bobbin? It could be warped or otherwise damaged but not that you would visually notice. That could also be the problem.
Finally, I do occasionally have this problem when I am running Superior bottom line in my bobbin. I need to tighten the tension on the bobbin case just a wee bit.