I had that problem from DP4 all the way to GM3. Did a clean install of Yosemite (14A3899) via MAS yesterday and the problem is solved. I think it had something to do with the old preference files.
I tried everything I could think of. Nothing helped, although I am sure a clean full re-install would do it.
I installed the Parallels Desktop App update to 10.1. It installed a safari extension. Now overtime I open Safari, it gives me this:
"Your Safari Extensions have migrated. You can choose the extensions you want to use in Safari Preferences."
If I click Open Preferences, it shows a list with only "Open in IE"....This gave me slight progress, If I now install a safari extension, it still goes away, however the Open in IE remains in the choices, but disabled. I manually edited Extensions.plist, and now my other extensions appear inside the list as well. (all disabled), now I can click to enable them...
I am wondering if there is ANY way that Parallels caused this, or is it just a fluke? Now that I think of it, I upgrade to Parallels 10 around the same time this appeared.