Hi,
I don't know, but you could try :
In System Preferences, Users & groups, Login items : delete Safari, then add it again.
If this does not work, try deleting the relevant .plist file :
~/Library/Preferences/com.apple.loginitems.plist
Did you readd Safari to the login items ?
(trashing the .plist has emptied the login items list).
If not, add it again, of course.
Strange indeed.
I would try to use "Maintenance" (Titanium software), just in case.
Uncheck these boxes before running it :
Spotlight index, Mail's envelope index, Web Browser caches and history.