Chrome Version 45.0.2454.46 beta (64-bit)
1Password Version 5.3 (530029) Mac App Store
1Password browser extension Version 126.96.36.199
Also tried with 1Password browser extension Version 188.8.131.52
I have two Chrome profiles, signed into one window each. Doing the "⌘\" command and choosing the login opens and fills it out on the other profile window. Clicking either the menubar icon or the Chrome extension icon and manually selecting the login fills it out in whatever profile is in the foreground.
Under Advanced in 1password settings, "Verify browser code signature" is checked, everything else is unchecked.
1Password Version: 5.3
Extension Version: 184.108.40.206
OS Version: OS X 10.10.5
Sync Type: Dropbox