Hi stu. My Windows 98se installation doesn't have either newdev.dll or program.exe. I wonder if perhaps you have tried to install a driver for a different version of Windows. Another possibility is that you haven't fully installed the motherboard drivers.
I tried a web search for newdev.dll or program.exe. One site where newdev.dll was mentioned said that it should be placed in C:\WINDOWS\SYSTEM and in C:\WINDOWS\SYSTEM32. The only references I found to program.exe suggested that it is used for "opening files of type URL:hypertext transfer protocol", and so shouldn't affect your usb ports.
What motherboard do you have? That may give us some more clues.