We've had the same problem for months; language editing works fine except for moodle.php and admin.php which are never successfully saved.
Our server has the suhosin php extension installed, and that appears to be the cause.
These lines were added to php.ini to resolve the issue:
suhosin.cookie.max_vars = 2000
suhosin.get.max_vars = 2000
suhosin.post.max_vars = 2000
suhosin.request.max_vars = 2000
It would be useful to get feedback from someone who knows suhosin and can suggest more optimal values for the above settings - they are probably quite high.