Thank you for your help on this.

It appears to be --disable-container that causes the problem.

I was also able to reproduce this on current git and a new config after only enabling focus follows pointer.

I did use them until recently when I wrote a sloppy patch to add an eesh focus set $WINDOWID command that does what next/prev do without unshading or raising the window like eesh wop $WINDOWID focus does. A bind uses the command to switch windows on current area sorted by their Y, X, W, and H values instead of their stacking order. It is easier to navigate back and forth when I can visually determine which window is next or previous from the current based on its location and size to the others. Maybe next/prev could have an option to do this sorting internally.

Sorry for the delay, I didn't receive an email for your reply. No, the programs do not matter, it happens with firefox and urxvt (a terminal). The upper window is opened with misc.place.manual_mouse_pointer and closed with ^W for firefox and ^D for urxvt. There are cases where it does focus the lower window, but I am unable to reproduce them. This is also an issue with latest git.

I can confirm it is fixed, thank you!