Don't want to be a messenger of bad tidings, but sometimes you can only get rid of a virus by fdisking your HD. I removed a virus from a pc once, reformatted the HD and bugger me the bastard virus was still there. Sometimes they hide in the boot sector. Not saying thats your problem, but something to be aware of.
If your seeing purple and and black squares I beleive this means you do not have the correct texture files, perhaps someone else can confirm this. I wonder if your re doawload of DOD had an error.