Can't switch Firefox windows using command+tilde
FWIW, I fixed the problem the following way.
I noticed that the ⌘+~ stops at a specific window, while works on other Firefox windows.
I closed that window, then re-opened it via History menu. The effect was gone, and ⌘+~ started working as expected.
For me, the problem was that the system shortcut was modified.
You should go to:
System Preferences > Keyboard > Shortcuts > Keyboard
Move focus to next window should be checked and contain the correct shortcut.