Please refer to this thread: http://ellislab.com/forums/viewthread/219220/
The situation on the production side is exactly the same - only the directories have changed from cwc_test and ana_test to cwc and ana.
As I noted at the end, I thought the problem “healed” itself when I accepted the changes to the index.php file on the control panel when I was testing EE2.5.2 upgrade. I updated the production system this morning, and I have the same problem. I thought if I forced the control panel to recognize that the index.php file had been changed again, I would get the message, click Accept and everything would be alright. But, not…
What else could it have been? I am really nervous about hoping for divine intervention on the production side! Suggestion on what I can do?