The 1Password Bookmark feature presents an "choose application to open the link" dialog every time, and then after choosing Chrome, it just opens a blank tab.
1Password is fully operational on my machine, and Alfred web search also works with Chrome -- so I think this is limited to the Alfred/1Password integration.
OSX 10.11.1
Alfred 2.8.1 (425) + Powerpack
Chrome 46.0.2490.86 (64-bit)
1Password 5.4.1