i've used black batting plenty of times, never caused a problems, works just like white or natural. i have had plenty of thread that just would not work...i was so upset one time when i bought a cone of machine quilting thread at a quilt show for $18 and as far as i'm concerned it was garbage! it broke every 2-3 inches...and even broke easily just giving it a tug...i called the company...they said sometimes if the thread has been sitting around a long time...or got wet...or what ever.(they were not admitting any responsibility)...it was not usable...even though it was a name brand, expensive and new...as soon as i changed the thread...no more problem.
when i run into this the first thing is to make sure it is a new needle, if it's not start with a new needle, then rethreading from the beginning, if the problem persists...yup, sorry gotta change the thread.
i have found i can buy 5 spools of the same thread on the same day...and one of them is not going to work in my machine...i just save those for hand sewing (unless it's really weak, breaks too easily by hand) or basting...and move on to a new spool.