I did’nt dig too deep when I found this bug. I reproduced this warning with theme and plugins activation and I switched back to the old file from 1.2.7. But it is more than possible that the problem occuer with other section of the admin area.
Using the old version of the file doesn’t seems to have any side effect though… So it can be considered as a quick bypass to stop the warning… Not a fix, but at least, it’s working.