Ok, now recently I've been unable to run a program without
CurrentControlSet\Control\VirtualDeviceDrivers. VDD. Virtual Device Driver format in the registry is invalid.

Ive been http://support.microsoft.com/default.aspx?scid=kb;EN-US;314452 here and I've followed the instructions, only now nothing happens when I try and run a program.

Is it anything to do with the "Command.com" as I am not sure what to do with it.

I had the same problem. If you go to www.google.com and enter vdd format invalid and hit search, it will give you "how-to" fixes. BE VERY CAREFUL when you do these as you're messing with the registry!! The 2 I used (both say same thing) were from MapInfo and MicroSolutions. There was also a link to Microsoft to tell you how to back up part/or all of the registry first. Make sure you edit the entry in "CurrentControlSet". I did the wrong one first (good thing I copied my key first) and it didn't work. When I redid the correct one, it fixed my problem... good luck.