You said you changed everything when you loaded the quilt- its always best to do a practice with the same fabric, batting, thread, needle to set your machine up for your project. I've not heard of batting with scrim causing skipped stitches.... Warm & natural is pretty popular batting. Your needle needs to be the right size for the thread being used. If you changed back to the first needle and it still happens I would recommend switching the thread. I've found thread can often cause lots of problems. Not all machines like all thread.