I find that when I have skipped stitches in machine quilting, if I lower my quilting pressure foot lower to the fabric so that it barely brushes against it, I no longer get the skipped stitches.. I notice that when the fabric has space to bounce, it will skip stitches. So I'm thinking that if your pressure foot was down close enough to the fabric to let you go over the thicker seams with ease (in moving over it) then it probably isn't down close enough overall.
So, coming up to a thicker seam, the fabric will bounce more, and again right after it.