Windows 7, Firefos 14.01, 1Password 3.9.5 and 22.214.171.1246
This problem started after the upgrade to Firefox 14. Setup: open Firefox, open a second tab, drag the tab to form a new window, open any website, shift window focus back to the original Firefox window. Open a url that requires a login and use the keyboard shortcut to activate 1Password. The focus shifts to the second window and 1Password tries to enter the information there, not the window requiring the login.
This happens with multiple websites in either window. It does not happen if I use the 1Password icon to activate the login and tt does not happen with the keyboard shortcut in Chrome 20.