I found a very blatant error in my php.ini file which caused this very symptom, eg. some php.ini settings did not take effect..
As of php7.0, the # character is not a valid comment starter. Only ; is accepted. But still many editors, for example vim, show characters after "#" as comments so you may not recognise that a certain part of the php.ini file is not an ignorable comment.
In my case, the php.ini filed contained this:
# ""
max_input_vars = 3000
The max_input_vars = 3000 did not take effect because the previous line is not a comment. It has some side-effect which causes my next line to be ignored.
Changing it to
; ""
max_input_vars = 3000
solved the problem.