Start up Megatune only, no terminal program. Select in the File menu 'off line'. Connect serial cable to ECU and PC. Go to the Communications menu, Select settings, then select the com port that you are using and click to test button. If it does not return a 'success' message, the com port is miss configured or the wiring is incorrect.
Once you recieve a success message, you then need to go back to the file menue and un check the offline selection.
The 'serial' port on nearly every PC is com1. Do you have any other software running in the background on your PC that might be grabbing com1(mouse, mobile phone, sat nav for example)? Have you tried another PC?
What is the exact warning/ error message that Megatune throws up? Screen capture and post a pic?
IIRC firmware after 1.0.79 use 19200 baude (AIM enabled firmware) and everything before was 9600.
Also, if you do not know what firmware is in the ECU, Megatune wont like the wrong version. Can we please see the error message?