I have had a couple of customer sites that display
The theme registry has been rebuilt. Turn off this feature on production websites.
And I couldn't seem to disable it. I tried every trick I found on the support pages and still couldn't solve the problem. I could click the checkbox and it wouldn't toggle, and updates to the Zen subtheme didn't make things better.
Here is the real issue: There is a misalignment of the checkbox and enclosing div. Clicking below the checkbox toggles it and, voila, the theme registry is no longer rebuilt.
I am going to try and find the solution to the misalignment, but for now I am just happy that my customers don't have to see that message.
I hope you find this tip useful and that you can spend less time tracking this down than I did.