If you use these two lines in my.cnf, I find that it works fine. This will log all queries to the server, from any source, not just PHP/PHPMyAdmin. Paul...
[mysqld]
general_log = on
general_log_file=/users/ugrad/linehanp/mydb/logfile.txt
Be careful though - enabling the general log can place a heavy load on your server. To be used sparingly for short periods/debugging only.