You are sure that the needle is going down, but a stitch is not forming (as opposed when the needle doesn't go down at all in that spot)? For the first case, the most likely cause is that the needle is flexing so that it is not in exactly right position for a stitch to form. This can be because you're pulling the fabric too fast, and therefore the needle is getting pulled out of position. A larger needle is less likely to flex, so this often solves the problem, as does slowing down while you're quilting.
However you seem to be having the problem only on one fabric. If it's a very tight weave, like a batik, it may be grabbing the thread. In this case a smaller needle and/or smaller thread might help. Or it could be that something about this fabric causes it (the fabric) to not want to lay as flat as it should while the needle is going through it. In that case, a larger presser foot or more pressure on the presser foot might help. Using a straight stitch throat plate, with a single small hole, might also help.
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If you find that the needle is not actually going down in those areas where your stitches are skipped, then the causes would be entirely different. If you have a Bernina with the BSR, it might be that the BSR is unable to read the movement of that fabric, causing it not to make stitches. If you are doing free motion without a stitch regulator, you might just be moving the fabric too quickly (however that is not the likely cause, since you are having this problem on only one fabric.)