Thanks Again for pointing me in right direction:
Even though I set .Retroarch to 777 it still would not act like it could write why i did uninstall. That’s only weird thing that bugs me. Its like th folder permissions were corrupt.
What I did to fix:
Uninstalled Retroarch via Cydia
ssh to ipad removed .Retroarch
Reinstalled Retroarch via Cydia
Set all Permissions to 777 rwx Group Mobile 501 Owner 501
Reconfigured Global Config
-Its now working as it should. Did IOS 7 change folder permissions by Default?
Note: All Bios fies must be recopied to ipad if you delete the .Retroarch folder
I just posted my steps in hopes in can help if someone else runs in to similar issue
Now working on removing the overlays and I am set
-Thanks again