Nightly Build # r48958, is the last version that woks with 1Password 3.0 beta-49. the 2 versions that are newer seem to disable the1Password plug-in.
Please look into this. I have also contacted the makers of 1Password on their Twitter Account. Thanks guys.
I can confirm that this issue. It also impacts browser extensions like Evernote.
Any problems with unsupported Safari extensions should be reported to their developers.