I recently had this same problem when quilting my DGD's quilt. I finally discovered what the problem was. I was using prewound bobbins, and perodically the thread on the bobbin was crossed and became too tight, that caused the tension on the bobbin thread to pull and the top thread to birds nest. Sometimes the thread would pull loose, and sew on ok. I finally figured it out after the bobbin thread broke a few times and I actually saw the crossed thread on it.
Anyone else have problems with prewound bobbins?