I am sure this has happened to people but i can't seem to find the solution

I had to buy a new HD for my Macbook Pro, i reinstalled the OS and went through the setup then installed Snow Leopard.

I then set about using migration assistant and all seemed well. I can now log onto my old user account and retrieve everything.

There is only one problem. I can edit and save documents i.e. word, excel etc...

But then every time i log out and back in my dashboard is the same as it used to be, Safari deletes my history and any new bookmarks i have saved.

Does anyone know why this is happening?

EDIT: Also when i book up it brings up 3 finder windows and safari like it used to, no matter what i do to tell it not to it does when i log back in.