I think that's the nature of the beast with thick seams/handquilting. I generally press my seams open and it does help quite a bit. But I've been known to do one or 2 stitches in areas where there are thick seams as well. I generally try to make my quilting design such that I don't have to go over heavy seams but it doesn't necessarily always work out that way. With practice, you'll get an eye for getting a single/two stitches the same size/consistency as your others.