Comment 5 for bug 1853039

Your nightly build is quite old, please update to see if the issue has already been fixed.

I still can't recreate it from scratch, and I can edit the keepout area to include both layers.

There is something strange with the file provided (doesn't match the one created from my testing following the instructions). It contains two keepout zones in the same location, with different layers. Has the file been edited outside of KiCad (ie a text editor) or something else (e.g. keepout copy/pasted from another file?)