I don't quite see what you're getting at, but it sounds like you're assuming that cwd() will return the directory that the CGI script is located in. This is not the case. The value of cwd() is dependent on your web server configuration, and you cannot depend on it when calling a script through CGI.

If each script should have its own log file, then provide a method in your module that takes an argument specifying the location of the log file, and each script can then specify its own.