Not sure I understand — what same file, what other form?

You have a CGI script that receives a parameter named "newvalue" via HTTP from a form.  You said "If I print the value its fine", which means the CGI script is apparently receiving the parameter as intended.  Also, you seem to be able to update the config file in principle (as you implied above) — but maybe not from the CGI script...(?).

In other words, what remains as a possible problem is my original suspicion that the CGI/webserver user might not be allowed to write...  So, have you checked the permissions?

Or, put differently, is your problem that the file isn't being updated at all, or that the file is updated but the modified value is not what you think it should be?