I have Updated My CRM Ent 11.03 To 12.00

Have you tried using the clear server cache option?

Yes

You need to ensure the files have the correct permission. CLI usually changes the user and permissions. 

I've had that before.
Did you run the specific "rebuild config file"? That fixed it for me.

If that doesn't work then check permissions as Rodrigo Manara said.

I use this from Sugar root to repair permissions on all files and directories after every upgrade.

sudo chown -R  apache:apache * 

sudo find . -type d -exec chmod 775 {} \;

sudo find . -type f -exec chmod 664 {} \;