This is a change in recent builds. This has always worked normally before now.
Chrome (47.0.2526.106 (64-bit))
Two user profiles (Home and Work)
In whichever profile is opened first, the hotkeys work normally.
On the profile which was opened second, pressing ⌘-\ opens the selection menu, (I have ⌘-\ set to "Open Mini" not fill automatically), but the pre-filled entries are incorrect, and selecting one of those entries or typing a new selection will not fill the fields on the page.
1Password Version: 5.5-BETA33
Extension Version: 188.8.131.52
OS Version: 10.11.2
Sync Type: Dropbox