I copied in the /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -f "/Applications/1Password 6.app"
line into terminal, rebooted and nothing changed. Not the worst thing in the world but annoying.
It would be nice if I could find where the bookmarks are kept and maybe change the icon, but that's probably not possible.
If anyone can think of anything else, I'm game.
Thanks for the help people. I'm glad I found this forum!