I use 1Password with Safari extension on 2 Computers, both OSX 10.9.5 and Safari 7.1
On 1 Computer (Mac mini 2012) it works, on the other (Mac Pro 2010) the extension sometime works, sometime works not (no pop-up)
I can't find any reason for that.
You've supplied the Safari version, could you let us know what version of 1Password and the 1Password extension you have on each machine as well please.
When it isn't working on the Mac Pro, is there any sequence of user actions that you're currently using to get it to work?