Perhaps goto the Warp9 site (http://www.warp9td.com/index.php/sw) check that you are using their recommended version of Mach3 and their lastest plugin. Download and run their SCU and follow the onscreen instructions (there is also a video showing how to use the SCU, if required).
Hope this helps.
Tweakie.
I think what may have happened is when I installed M3 I did not restart the puter. In the M3 manual it says this can create problems. I restarted after I installed W9 Smoothstepper. According to the documentation Mach can get screwy if not restarted after install.