My PC8500 sometimes leaves a pretty long piece of bobbin thread when it runs out, and sometimes that will pull to the top when I start again. Are you sure it's the new bobbin thread coming up? Seems weird that it works fine unless you change the bobbin in the middle of a design. Do you have to take the hoop off to get to the bobbin? If not, maybe you aren't getting the bobbin in quite right, or the thread in the tension quite right. I know mine is sometimes hard to get the thread in right because the embroidery arm is in the way.

Christin -- take your bobbin out and put it in correctly - this will probably take care of your bobbin thread coming to the top. Make sure you also bring the bobbin thread out in the correct manner - I have a Brother PE 770.