Hi Ugotit,
I honestly mean you no offence but you have to trust me on this one - it is not the Mach3 software that is causing you the problems it is your basic understanding of exactly how to use the software which may be at fault.
May I respectfully suggest that you take some time to read the Manual and other associated documentation
http://www.machsupport.com/documentation.php which will provide the answers to the questions that you have raised so far and perhaps give you a better insight into setting up Mach3 for use with your machine.
To be totally frank – the machine controller you have is bit of a handicap to you mainly because of the lack of support and documentation provided but it must, to a certain extent, be lacking in quality for two of the internal boards to burn-up.
This raises the question – has the LPT port of you PC been damaged as a result of the burn-up ?
What Windows operating system are you using on your PC ?
Tweakie.