I am using figures with contour lines, thus my figures are: axes > contourgroup > patch objects.
In my exported images, I was getting the axes with all text label objects but no lines.
I had to change line 97 in isolate_axes.m from allchild() to findall() as a fix. I don't know if this breaks anything but it shouldn't as findall just finds all objects lower in the hierarchy than the one passed in, which is the axes handle in this case. I was losing the patch objects that make up the figure as allchild() was only returning the objects at the first level under the axes.