With the most recent Creative Cloud update I've noticed that the Shape Builder Tool still allows merging/cropping/deletion like in previous versions, however alters the inherit path structure of the shapes that remain after the edit. This is one of my favorite new additions to the tool set, however with this new behavior it has become quite cumbersome (and nearly impossible) to use and has me wondering if there is a new default setting that is messing me up.
I have done some initial research on the problem and haven't found anything of much use. If you could let me know if this problem is somewhat common or a possible fix, I would greatly appreciate it. Thanks!
(Attached are a couple screenshots of before/after a simple shape edit with the tool.)
Before
After
