Been there, done that. I long ago decided that life was too short waste wrestling a big quilt through the throat of a small machine. AND that it was absolutely NOT fun, that quilting was a hobby, and the day it stopped being fun, I was done with it. So now I make my tops and quilt by check. (ie, send them to a long-armer). Makes things MUCH happier!
But if you truly do decide you have a masochistic streak, good luck. Oh, you won't have the nests if you pull your bobbin thread to the top at the beginning, and hold both ends of the thread as you start.
Another cause might be that the bobbin is not threaded correctly, or the thread has slipped out of place, or that the top thread is not threaded correctly. Also, replace your needle regularly.