Please try these resets if you have not already.
1. Reset NVRAM/PRAM. http://support.apple.com/kb/PH18761
2. Reset SMC. Choose the method for “If the battery is non-removable”.
https://support.apple.com/en-us/HT201295
3. Start up in Safe Mode. https://support.apple.com/en-us/HT201262
Once in Safe Mode, click the “Restart” button at the bottom.
4. Delete com.apple.Safari.plist file and test.
Empty the Trash.
Quit all applications.
Hold the option key down and click the "Go" menu in the Finder menu bar.
Select "Library" from the drop down.
Library > Preferences > com.apple.Safari.plist
Right click on it and select "Move it to Trash".
Close the Finder window.
Restart and relaunch Safari.
If this doesn’t help, “Put Back” the com.apple.Safari.plist
Right click on the Trash icon in the Dock and select “Open”.
Right click on the com.apple.Safari.plist and select “Put Back”.