Hi there, I’m actually having the same problem. I haven’t been able to use the Header builder for any of my websites because the hide at certain breakpoints feature has not worked.
See this screenshot:

In the screenshot, the inline navigation (the element being inspected) is not supposed to be showing at all in any breakpoint starting at 979px and below. As you can see, I have selected the 768px - 979px breakpoint with the mobile preview button in the PRO Builder menu. It should not be showing at this breakpoint, yet there it is, clashing with the mobile menu.
Here is a second breakpoint that the inline menu is not hidden from (this time 481px - 767px):
==> Link to the second screencap
What can I do on my end to fix this?