I had a similar issue and it turned out my top thread had come out of one of the guides without me noticing. Seemed really insignificant but re-threading fixed the issue for me.
Of course, I didn't even NOTICE the problem until I'd quilted the ENTIRE quilt, and it was one I was rushing to get done in time to be a Christmas gift. Darn Murphy and his Laws!
Good luck with your nest removal...not envying you that job. Been there, done that!