I have customs @windows hidden + one @win not hidden, regardless of what is the active window, if I click on the Window menu and select the @win that is not hidden, it shows one of the hidden window instead of the @win.
Setup just in case: first status window has one channel, second has 3, third has 2, fourth has no channel and only custom windows

Note that my hidden windows are non desktop while the non hidden window is desktop, Talon mentioned that he could not reproduce the issue with a desktop non hidden window + non desktop hidden window, but said he could reproduce when none were desktop.

Thanks this issue has been fixed for the next version.