The checkbox "default" defines which group becomes active when new window is created - that's when "Separate group for each window" is activated. I just checked - chosen second group as "default" and new window immediately got it.

Why do you check LEDs for the active group? What does the indicator applet show?

I'm sorry, I can't remember why I was using the LEDs to check, or what I meant by that.

Now you've explained it, I understand how it works. I'll update the user guide to explain.

Technically, this is NOTABUG.
But there are a number of usability problems with the 'default' checkboxes:

1. They shouldn't even be checkboxes, since only one can be selected
2. They are dependent on the "Separate group for each window" checkbox lower down being selected. It seems wrong that they are above it.
3. There's no visual indication that they're unavailable when the "Separate group for each window" is unselected

1. They are radios now
2. The "separate group" checkbox is below the layout list just because his has lower semantical priority.
3. Good idea, I will consider disabling these radios.

3. Sorry, it is already there - I forgot:)