I'm working with one file, let's call it the FILE A.
I'm activating the "Align and Distribute.." window. It' works fine.

Then I'm hit Ctrl+N and I'm creating new instance of Inkscape, let's call it FILE B.
I'm copy some graphic from FILE A to FILE B with no problem. But then, when I'm on FILE B I'm activating the "Align..." window, it...switch me to FILE A

I've try it many times and I couldn't align or distribute on FILE B ?! It's always switch me to FILE A.

Is it normal behaviour ?

I think that's a window setting to have the panels dockable or float, or somewhere related to your desktop settings -your operating system may make it clearer. (It works fine here.)

When I've switch to dockable, everything works properly.
So I guess it's a floating windows' bug.