Answer from Autodesk Enterprise Priority Support:
"Thank you for creating a case with Autodesk Enterprise Priority Support.
It appears that you are using the classic version of the hatch command (eg HPDLGMODE=1). This dialog box behaves differently from the ribbon version of the command, in that it does not regard the layer settings for your drawing. In the ribbon version of the command, it will show layer settings from the layer dialog box. For example, if you have a filter active, the ribbon will show you the layers included in the filter. The classic Hatch dialog ignores these filters and "does its own thing" with regard to sorting.
I hope this helps! Let me know if you have any additional questions. "