I'm guessing there's a mismatch in the bobbin tension and the upper-thread tension on your machine. Try adjusting the upper-thread tension and sew a few lines of stitching on some scraps. It also could be to some 'stickiness" of the fabric so that the needle/thread don't pass through smoothly.

That puckering is not normal. If the ironing takes it out and it stays out, then no worries.

The smaller box pleats look good!!!