"Had the drive repaired"
Did that by any chance involve a visit by a tech? If so, he may have not restored the machine back to its proper state after using Windows for some tests and so on. In that case you would need to contact the company.
AFAIK most DOS based controllers have a line in the autoexec.bat file that calls another file to load the control software and my first suspicion would be that it was commented out by putting "rem" in front of the line that calls up the control software.
There is another possibility. Is there a screen message during bootup that says press xxx to select startup options? In that case there might be a choice in the BIOS to select either the control system or Windows as the default and it was left in the wrong state. The actual choice for the control system would be DOS and the autoexec file would load the software and any necessary drivers.
EDIT: Just read your latest post. From Windows select Start .... Run ..... and then type "CMD". That will bring up a command prompt window where you can use DOS commands to list files and directories, and generally see what is going on.