I'm wondering if it has something to do with the way you hold onto the threads when you are starting out. For example, if you are holding them up, maybe try holding them more parallel to the quilt? Or perhaps hold the top thread with more tension on it than the bobbin thread? I'm not sure what you mean by the bobbin stitch coming up. You mean there is something wrong with the first stitch you take after bringing the bobbin thread to the top?