Looks like the answer or source of the issue is in the User account, for Safari
troubles in your Yosemite. There's a tedious method to generate long cryptic
command-line Console logs in which some bits may mean something to an
expert who could find intelligent purpose resulting from incomprehensible lines...
When the issues occur, there is a corresponding Console log (or dozens of them)
sometimes per second, in various system sections, some in duplicate, in OS X.
Maybe this thread may catch the attention of ASC discussion regulars who have
a good grasp of the Console logs and may share a method to extract those; or
at least divine simpler shortcut methods to 'whack the ghosts out' of the machine.
At least overall, it seems there may be an answer in some aspect of the Safari
and user preferences, privileges, with maybe some corruption involved too.
Was there any Safari extensions installed? Some of them can be bossy, when
from a third-party source. A few adware items also can affect Safari settings.
The Developer setting for Safari may enable other settings in the Yosemite version
that may (or not) be helpful; the standard feature I had used most often was Reset
Safari, to wipe out many items saved that didn't need to be kept in between uses.
If Yosemite's newest Safari version hasn't that available, it'd be a strange loss.
Hopefully this topic can help others who find it and are willing to dig into -but not
destroy their system- to find the odd cause behind this settings problem.😎