Virus infestations MUST have a root system to redeploy upon reset of the computer, or deletion of portions of it's code. Desktop.ini is a "built-in" area virus' can use as most folders never have a desktop.ini assigned to them. Also, they are a windows hidden file by default, so most users never have an inkling about what is happening right in front of them. The key to discovering which "might" contain code is to find out if the file is protected from deletion. Easy way to find out which are protected is to do a search on C:\ using "desktop.ini". Just use explorer to do this. Once found, highlight them all (can be over 200 on some systems) and press delete. Odds are good you will find many which will not delete. Now you need to ask yourself, why? Desktop.ini files will be recreated as needed, so there isn't any reason to lock any of these files, except one -- To protect it. If they do not need protection why do they and who or what assigned their protection? System files are often protected, but destop.ini isn't considered a system file ever.
People need to realize their computer is not their own. Simple fact of life. Now how much of your computer you want others to use for "their" purpose is the real question here. By far, the highest percentage of all malware is to help these "others" promote their products, goals, or desires in some way or another. One really good way to do this by keeping tabs on your every computer move. Can't do this by cookies alone, so PUP's are the next step, and it goes on from there.
I regularly clean up my windows system, most of the time from a linux boot. I have multi-layers of protection that start at the modem and end with me and everything you can think of in between. Yet I am ALWAYS infected to some degree. Believe me, you are too! Even Microsoft does this themselves with their windows products -- They always have. They are perhaps, even the most aggressive at it, because they build it in the Windows product. They also provide the many of the useful tools most hackers use, right in windows. So it's just a matter of finding a way to slip in, and that isn't a problem at all in just about any system. Tools are abundant and free (mostly) to do this and not at all hard to come by over the internet.
When someone tries to convince you, you are not infected, leave politely, but leave and find someone who actually can help. Far too many "trust" what is given to them, as long as it is something they are hoping to have. Truth is, any form of malware should go squarely against that "trust" and should tip you off to go in a different direction then they are trying to provide to you.
Since 1969 I have been involved with computers and have seen all of it personally. What I know today, which I did not know 15 or 20 years ago is, you will never win the war fighting off malware, you will at best, win a battle. Most of the time you will be doing good to fend off the battle for a later date.
My 2 cents.